I've lost save files of AC:Black Flag when re-installing Windows. Anyway to recover them?
(Disclaimer: I have not played this game.)
Uplay has a cloud saving feature; if this was enabled, then running the game should download the missing saves (or at least provide an option to do so). (Note: apparently it has had a long period of downtime, and there seems to be some confusion about whether it is currently active.)
If cloud saving was disabled (on your or Ubisoft's part), then there is almost surely nothing you can do. Deleted files can theoretically be recovered, but only so long as nothing else has been written to that part of the disk. Reinstalling Windows is highly likely to have trashed some or all of that data, and even if it hasn't, the old file system information is bound to be gone, so it'll be effectively impossible for you to locate the right areas, even if you were to look at every single bit on the disk.