Well, the files in premod's contrib/ are only the files modded from phpBB3.0.6 to premod 3.0.6, so of course there are a lot fewer changes than from 3.0.5 to 3.0.6.
Here (Prosilver / subsilver2 code changes
) you'll find an update file listing changes between premod3.0.5 changes to premod3.0.6. These does not includes phpBB3.0.5 to 3.0.6 changes either, they are meant to update the SEO code on an up to date them (as far as phpBB core).
The idea is to first update you theme using phpBB.com code change for styles, and then to apply our update for our code.
Or, the full story is to be found in the premod update packages, which all takes care about phpBB and SEO code update at the same time.
If you theme is based on prosilver, you can just winmerge it with the latest premod's one, should not be that hard to keep your modifications.