After my swim this morning I synced up my Swim with my MacBook Air like I always do. When I launched Garmin Express, it forced an update on me. When the update & sync were complete, the activity was in Garmin Connect online, but the FIT file was not saved locally where it usually is. Was this a change in the new release of Garmin Express? Is the file being saved in a different folder now?
This FAQ has the updated location of backed-up FIT files when using Garmin Express: Why are my activities files not being stored on my computer once I have uploaded them to Garmin Connect using Garmin Express?
If you checked that location and still cannot find the activity, can you perform a dummy workout on the watch (5-10 seconds) and see if that file is backed up after successfully syncing with Express?