Is it possible to keep playing a saved game if a regular patch overwrites one of these files?
Ok, I'll try to explain, what happens, if you install a new patch and you had FlavourMod installed for a previous version before:
FlavourMods adds some variables for handling temporary Features and Bonuses that need saving in CvGameCoreDLL. As soon as the number of expected saved variables differs from the number of variables saved in the saved game your game will break.
In case CvEventManager.py was overwritten, End of Winter will fail, but save games should be ok, but it'll probably stop thawing.
In case CIV4GameOptions.py changes, the dll needs to change too and you'll most likely encounter the problem explainded above.
In (my) theory, the FlavorMod is only effective during map generation, right?
Not any more. It's true for Flavour Start, but not for End of Winter.
Although I faced the problem that my last saved game wouldn't load (it killed the Civ EXE-file on load somehow, starting a new game did work though). Maybe because I installed the k-version of Flavour over the l-version of FfH?
A new game might work sometimes if you do it that way around (install the new patch and install the old FlavourMod afterwards). You'll lose all fixes and changes of the new patch connected to the three files above though. It should even be possible in many cases to load saved games from the patch before, if you had FlavourMod installed then too.
Conclusion: I don't recommend installing FlavourMod for a version it wasn't made for. Something will most likely break, even if it's not apparent immediately. If you don't want to play without FlavourMod, it's probably better to wait for a compatible version before upgrading your FfH. To make it easier to find the currently supported FfH patch I'll add a link to the patch needed for the current version of FlavourMod to the first post in the future.