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All previous progress was missing. I'm not sure what OS you are using, I am playing on Ubuntu Linux 12.04 so my directory structure may be different than yours.
What I found was that my previous progress file was in
home/username/.local/share/fasterthanlight
while the new current progress file was located in
home/username/.local/share/FasterThanLight
The progress file was called ae_prof.sav
On linux, the capitalisation in the folder makes a difference, not sure about Mac or Win.
I renamed the current ae_prof.sav to back it up, then copied the old file into the new folder.
This recovered all my old progress.
I have a suspicion that on OS's that treat capital/non-capital filenames as being equal, the new folder name may have over-written the old folder name, erasing the old progress file, but that is a guess.
Hope you manage to recover your old progress, good luck.
Steam should have prompted you to overwrite though.
No sign of any older my documents folders. What is really confusing though is that, if I'd wiped the save folder out then I should have NO progress. But about half the ships are unlocked. Very strange. It's like it's loading my game from a year and a half ago.
btw, there's two files in 'fasterthanlight' :
'ae_prof_new.sav' modified today
and
'prof.sav' modified in 02/04/2014
I found another 'my documents' folder on my comp I didn't know about. But it has an empty 'my games' folder. I wonder if something has been merged and overwritten without my knowledge when I was unpacking win7 to get a new explorer file?
Would saves be different when I load steam up 'as administrator'? Because I sometimes do that to get civ5 working..
I remember when one ran Advanced Edition for the first time and already had a pre-AE profile file in My Documents it created a ae_prof.sav that included your unlocks and stats.
Maybe ae_prof_new.sav is created in the event that the game doesn't find ae_prof.sav, but does find prof.sav and it is not the first time AE is run.
Not sure this info would help you though.
I've got a horrible feeling this is unfixable then....