I understand that the JS version is a port that's been rapidly catching up to where the legacy flash version was as far as content. When the two are finally caught up, is new development going to continue on both or will it solely be the JS version?
JavaScript is the only version in development. The only updates Flash will receive are to fix bugs in the save conversion functions. Even that's in question.
I like the legacy version because I know it's compatible and easy to use with TiTsEd, but when I finally hit the end of content, am I going to have to figure out how to transfer a save file over, or if that's impossible, start over from scratch?
Can you run CoC 2? If so, you can run the TiTS JS version.
There is someone working on a JS Save Editor. In the meantime, it's actually surprisingly easy to use console commands to directly modify most things.
The Flash version has 'Export' and 'Convert File' buttons on the Save/Load screen that will convert your saves to a format that can be read by JS. There are a handful of bugs (that I know of), however:
1. It ignores your equipped Accessory, effectively deleting it.
2. There seems to be a problem with lip mod.
3. Genitailia revert to Pink Human (might be a general bug with tail genetails, rather than a conversion issue).