We just went through a very frustrating experience investigating some disappearing hotspots. The hotspots were visible in Sketch, but not showing up on Invision. Occasionally, hotspots that had been on an artboard for some time would suddenly disappear from Invision. After much troubleshooting, we discovered that this could be fixed by re-uploading the missing hotspot's destination artboard, even though that artboard had not been changed. To do this properly, we had to go into sync settings and disable the option, "Prevent upload of unmodified artboards".
Even though we were able to fix the problem and continue using Sync + Prototype, this issue has definitely eroded confidence in the tool.
We're on Sync + Prototype 2.3.79