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I'm planning to start a new playthrough of TW1 using the Flash Mod. Afterwards I want to import the savegames of this playthrough into TW2. Can I import such a savegame safely or does the Flash Mod cause problems?

If it does, I won't use the mod.
I know a number of people who used the Flash mod and none ever mentioned troubles importing. W2 just imports a few flags from the first game, so I can't really think of any reason why it wouldn't work.
Okay, thanks for the clarification. I just wanted to be on the safe side concerning this matter.