Further to my post last year about retrieving GPS data from corrupted Garmin fit files, when it happened to me again last week due to a failed battery I came across this tool: http://fitfilerepairtool.info/

It does what it says on the label and makes repairing a corrupted fit file a fairly simple and painless operation. Though you do need Microsoft Access or the Access runtime (which means a windows install) so it’s not quite right for everyone (luckily I have a Windows image with Office Pro running in VMware on my MacBook).