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How are you launching both instances? Are both launched by double-clicking, or the panel or ...? Do you have any executable properties set?
Perhaps it is a Qt thing? Do other Qt apps act the same way?
Please use your task manager and check if the two versions of Sigil overlapped in any way? Perhaps turning off the damn Windows Efficiency mode would help? Perhaps Windows itself is sleeping the other instance of Sigil?
I do not have a big enough test epub to try to recreate things on Linux. If you have access to Linux, you may want to test to see if it is an OS thing or not.
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