Modlist
player.log (I accidentally booted up the game again after recording the bug hence the -prev prefix)
https://www.youtube.com/watch?v=gvi_B6UTAZI
Reproduction steps:
1) Build the craft (part order doesn't seem to matter) with a SG-RV3 Heatshield, SG-RV1 Return capsule pod, SG-RV2 Parachute and SG-RV4 retro pack
2) Launch the craft (staging in the video is optional)
3) Revert to launch or do something to (presumably) reload the game
A smoke plume appears right before the loading screen ends, Heatshield now will lose physics and is said to be on a collision course with Kerbin despite being on the launchpad, and according to Kerbal engineer has a NaN apoapsis and infinity periapsis.
The revert to launch issue appears to happen with other probe parts (e.g the Transit 4A with the corresponding Injun 1 and Solrad3/Grab 2 satellites in which they seem to mysteriously decouple and disappear while reloading a quicksave in orbit, however I haven't tested this bug with other parts too much)
This bug does not occur on a clean install with purely BDB and its dependencies.
EDIT:
Uninstalling the mod "Routine Mission Manager" seems to have solved the issue, strangely enough