Question: When a Christian sins, how does he regain fellowship with the Lord? Is this an all or nothing thing (based upon 1Jn.1:9), with the filling of the Holy Spirit returning after confession (Eph.5:18)?
Response: Fellowship with God has both an absolute and a relative dimension; we believers are all sons/children of God, and that is absolute; however, we are all at different places in our nearness to Him (and even individually this ebbs and flows, although ideally we should all be making a continual and continuous bee-line directly towards Him). I think that's the point in 1st John 1:7 where it says we have fellowship with Him and with our brother/sister believers if we "are walking in the light" - we all need to be on the right road, responding to Him rather than rebelling from Him (i.e., we all need to be "walking in the light"). That is an absolute too. We can not be happily giving in to carnality with no concern for the fact that God is not pleased and expect to be on God's "good side". But to those who are "walking in light", there is clearly a lot of room for individual variation (we may not be walking in light as well as Paul did, as well as John did, as well as David did, etc.). As the One who empowers all the good we do, the Spirit is our supporter in all good walking, just as He counsels and urges us not to get off the good road and step out of the light, even temporarily, and the Spirit also prompts us to return to the light, if ever we stray into the darkness.
Confession of sin is unquestionably an important issue and an important practice in the individual believer's Christian walk.. The simple answer to your question on how a person regains fellowship with God is indeed "He confesses his sins". It is clear from scripture - throughout the Psalms and elsewhere as well as from 1st John 1:9 - that when one is aware of having committed a sin, then by all means it is necessary to confess that sin to God (e.g., Lev.5:5; Ps.32; Ps.51; Neh.9:2-3; Matt.3:6; Acts 8:22). 1st John 1:9 is thus just one verse of many that deals with this subject. What it says is true. What some may extend it to mean (especially if said extension/interpretation is done in a vacuum in the absence of other scriptures on the subject) may very well not be true - or at least may be misleading. There are a number of issues that come up here. For example, our attitude in confession is key. That is to say, admitting our sins to God presupposes that we are indeed owning up to our mistakes:
He who conceals his sin does not prosper, but whoever confesses and renounces them finds mercy. Proverbs 28:13 NIV
If "confession" becomes merely some rote exercise, then it is not worthy of the name. Between the one extreme of an over-emotional and even hyper-emotional self-flagellation on the one hand, and a cold, unemotional and not at all heartfelt cataloguing on the other lies the true path for confession. We have to approach this issue the way we would any other part of our relationship with our Savior Jesus Christ and with our Heavenly Father. Jesus is our Savior, and God is our Father. We have a true, living, vibrant relationship with them that is more real (and more important) than any we have on earth. We need to relate to them in a real and genuine way, so that with confession, as with all our other prayers, we need to commune with our Lord and our God in honesty and integrity, in true faith and love, seeking mercy and confidently expecting it as one would of any loving parent, as one would of any loving master.
If we sin, we should confess, and if we confess aright, we are forgiven and we are cleansed. As to the related issues you bring up here, however ...
1. I don't find any scriptural basis for assuming a 100% control of the Spirit state vs. a 0% state as the result of personal sin. Sin and sinfulness, like spiritual growth and a growing closeness to our Lord, are often trend-like. That is, in the case of sinfulness, it may grow and go from bad to worse. The Spirit works with us as long as we are genuine disciples of Jesus Christ. But we, by our bad decisions, poor choices, and unwillingness to respond to God's truth, often limit His influence.
2. I do not find any scriptural basis for this 100% "filling and re-filling of the Holy Spirit", at least not in the way it is sometimes explained especially in the Ephesians.5:18 context you mention. That scripture commands us to be full-filled by the Spirit - that is, to be led forward, to be motivated, and to grow more and more under the Spirit's influence day by day. It is not describing an absolute state.
3. I therefore do not find any scriptural basis for connecting "fellowship" with this interpretation of the "filling of the Holy Spirit". We have fellowship with God the Father through our faith in Jesus Christ (1Cor.1:9; 1Jn.1:3). Like any other relationship, the fellowship we have with Father and Son depends upon the state of the relationship. Sin clearly harms it. So does apathy in studying the Word, a lackadaisical attitude toward prayer, being over-focused on the world and the things of this world instead of on the things of God. The Spirit is our great help and Helper in building and enjoying our relationship with our Master and the One who sent Him, but we have to pursue this relationship. Short of making it our top priority, it will never be all that He wants it to be - and that is true even if somehow we could otherwise keep ourselves completely free of sin.
Clearly, sin separates us from God, but that separation is not an all or nothing thing (at least not at first: cf. 1Jn.5:16-17). Indeed, we may often not even be aware that we have sinned (cf. the Old Testament offerings for sins of ignorance). At least one hopes that we will advance to the point where sin becomes less common and less overt, that we will become less prone to out-and-out offenses against God. Yet we will never become completely free of sin, even as we pursue the sanctification that we are required to pursue (1Ki.8:46; Prov.20:9; Rom.3:23).
I suppose the bottom line here is that we cannot (and should not) want to boil this matter of confession and fellowship down to a math problem. We confess to our heavenly Father the same way we might have done to our earthly fathers - it matters that we tell Him, it matters that we tell Him the truth, it matters that we understand what we have done that, it matters that we realize that He is not pleased with such conduct, it matters that we intend to do better (or at the very least, do not intend to continue on in the same behavior without even blushing). If we thought to act otherwise with our earthly fathers, it would be total nonsense (and they would not have been impressed by the fine print of some written contract that we might have thought to have had from some misinterpretation of their previous words). Our earthly fathers would not accept false, dissembling, disingenuous, or silly confessions over serious matters - why do we think our Heavenly Father will? He made fathers in large part to teach us lessons such as this (cf. Heb.12), and takes the Name "Father" to teach us something too. If we will be close to Him, have real "fellowship" with Him like we do/did with our earthly fathers in their many roles, then we have to take Him and everything He says seriously. To my mind, 1st John 1:9 is all too often used to avoid taking Him seriously, and that is clearly a mistake.
I suppose that is why I do try to adopt His attitude towards sin, but at the same time counting on His love and mercy (and remembering that Jesus bought that mercy for me). I try to spend some time every day in confession - given the vast sea of sinfulness to be found in every waking thought and conversation, one certainly does not have to wait for "willful sin". After all, if we know we are sinners by nature, odds are we almost always have something to confess.
Please see also these links:
Repentance, confession, and forgiveness (in Basics 3B)
1st John 1:9 and confessing sin.
I do hope this is helpful in some way.
Yours in Him.