Forum Moderators: Robert Charlton & goodroi
First, if you haven't already, I suggest you study this thread: Supplemental Results: What exactly are they? [webmasterworld.com]
The basic answer is yes, urls can gain a place in the "regular" index even after being tagged as Supplemental. But Google will not spider Supplemental URLs nearly as frequently as others, so even after a fix is in place, more patience is needed.
The other issue you raise is probably related to this: Google uses many different data centers and their data are not the same. Sounds like you first may have seen results from a newer data set and then it switched back. But after 2-3 years of next to nothing from Google, that glimmer of hope is probably an indicator that something good can happen for you.
Watch your logs for Google Search referers most of all - in a world where different people get different results, that's what counts the most.
The clean up involves using redirects or noindex tags for all the alternative URLs. These remain tagged as Supplemental for one year and then they are dropped.
There's also a matter of what appears to be redundancy causing some pages to go Supplemental, which is not the same thing as duplication or near-duplication.
I see Matt Cutts posted yesterday a reply [mattcutts.com] which mightbe of relevance to this thread:
...., PageRank is the primary factor determining whether a url is in the main web index vs. the supplemental results, so I’d concentrate on good backlinks more than worrying about varying page layouts, etc.
Thoughts?