I believe the Cleaning progress dialog comes up whenever Mend has a considerable amount of work to contend with. I used to see it occasionally, but I just don't tend work with source material anymore that's in such a state where I have to endure it. The files are typically huge where the dialog is visible.
Can you downgrade to Sigil 0.9.9 (or whatever version you were previously working with) and verify that the issue goes away when performing the exact same steps with the exact same source?
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