I'll bet they are still there. Look in the gpx folder and see if the gpx files are still there.
Yes, they were still in the GPX folder, but for some reason, they did not appear in the Geocaching/managemwaypoint folder.
Anyway, I downgraded to 3,90 again as I found the issue with the tripcomputer too big of an annoyance. Will wait for a more stable version (non-beta)