I had a user with a slightly corrupted FIT File. GOTOES has a standard set of automated repair tools in the merge tool. This is already built in as discussed here. I suggest you start there first when trying to repair corrupted FIT Files.
Since that tool was originally designed as a merger, it can't repair every type of corruption, so I have added a new tool that let's you look inside your FIT file displaying all of the known fields. It will also give you a repair button that lets you try and fix your file. Again, I suggest that you start with the merger tool as your repair tool, and then come to this tool if that one fails you. You can always run your file through BOTH tools, using the fit file viewer first, and the merger second.
Here is an example of me using the tools to fix this user's FIT file: