I'm not sure I completely understand what the problem is.
The activities aren't on GC, or the reports on the activities aren't on GC?
When you say the data is there, where exactly is it?
If you've synchronised all activities using Garmin Express and you can't see the activity on Garmin Connect you might want to open a support ticket.
This has happened to me twice in the last year with my FR305. What I found is that if I have problems syncing, when it eventually does sync, the map data isn't there but the summary is. I tried exporting a fit, a tcx, and a gpx file to see if I could retrieve it but the map data was gone for good (at least for someone with my skill set). It obviously got corrupted somehow.