You can cheat a bit with an editor like this one http://www.ftlgame.com/forum/viewtopic.php?f=7&t=10959 so that you can sync both your progress files with the same unlocks

BTW, you can get yoursel a makeshift cloud support for many GOG games by using dropbox/skydrive/google drive and some tools like GameSaveManager, which works pretty well

Not sure how much this helps, but the file prof.sav holds that info. On my computer it's in Documents->MyGames->FasterThanLight.

If you were to copy this file back and forth, you could conceivably carry the game back and forth between computers. If a game is in progress it's the continue.sav file in the same folder. So if you copy both, I believe you could even continue the same game across both machines.

This doesn't help with merging once you have games on both machines though. There is a thread on the game site for an editor that supposedly allows unlocking ships and editing saved games:
http://www.ftlgame.com/forum/viewtopic.php?f=7&t=10959&start=70

I have not tried this myself, but you should be able to at least unlock the ships that you have earned on the other computer in good conscience. (or even unlock other ships in not-as-good conscience).

Hope this helps!

Once synched up you could try this.

Awesome! Thanks for all the helpfull input! I'll report back as soon as I've had the time to fiddle around with the info you proovided.