Yeah, like you I sometimes do a Tweak ePub and Edit in Sigil at the same time (using Edit in Sigil to get easy visual access to the styles, and Tweak ePub to actually make the changes if it has an NCX I want preserved). Or I might start editing a document in Sigil and find it is a massive amount of work, but I leave Sigil open in the background and come back to it in stages, working independently (and restarting) Calibre in the interim.
I don't know what options if any I have around this. If I understand correctly Kovid is trying to make it "safe" for anything to read/write to support multiple access. Which in the long term will be great. The downside as I see it (without poring through the code) is that for everyone who doesn't do "multiple process" stuff, you still have to take the hit.
I'll wait to hear from Kovid before I push the panic button on this, but to be honest right now I am feeling rather ill for a couple of the plugins (and that I have less than two days before the next Calibre release goes out). I'm feeling a bit like roadkill at the moment.
