I'm not near a computer right now to test, but I want to be sure I understand what you're saying.
1) add/load existing html file
2) pre-existing css is automatically pulled in/created with #1
3) immediately run "delete unused css classes"
Are those the steps that will recreate the problem?
If so, does saving the epub first (before deleting unused css classes) eliminate the problem? Or saving and reopening first? Just troubleshooting, here, I'm not suggesting those as solutions to your problem.
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