I've been playing FTL on two machines and I needed something to merge the prof.sav file formats.
I went ahead and wrote a reader/writer of the prof.sav format in python before I looked on here and found ComaToes' great work on the java based profile editor (complete with the reading/writing code I needed but no merger).
https://github.com/ComaToes/ftl-profile-editor
A quick look at the java code seems to suggest that ComaToes' profile editor doesn't attempt to read/write the high scores. My merger makes a "best guess" at merging the high scores so that might be useful
I could port my merging code to java, but if anyone is interested my project contains a python reader/writer/merger
enjoy!