Well, that's the risk you take when you modify core Geeklog files. That's also why we suggest to put as much of your modifications into lib-custom.php as possible.
If you've modified your theme, then it shouldn't be too hard to update it for 1.3.6. The changes are listed in the documentation.
As for a list of changed files - well, there's always CVS but you won't find many files that have not changed. Geeklog 1.3.6 really is a massive update that fixes a lot of minor bugs all over the place and also brings with it some (I hope) useful additions.
bye, Dirk