OK, it doesn't really seem to be consistent. I've tried a few times now, and here's what happened:
- a second empty instance of Sigil didn't affect the clips 5 out of 5 times.
- a second pre-existing epub killed the clips in the first instance 4 out of 5 times.
- a
third instance of Sigil, no matter whether empty or not, killed the clips in the first and second instance 5 out of 5 times.
No idea if that helps. As I said, for me it isn't a biggie.