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No ideas either here. And as DiapDealer said there are *no* routines in Sigil to remove the entire Sigil Preferences folder. It is meant to stay as is across installations, upgrades, etc.
I would guess the culprit is some silly clean up or anti-virus program that was overzealous. Other ideas would be a network drive mounted incorrectly overtop things or you may have logged in under a different user name somehow without realizing it and are looking at two different places (same relative place but for different users).
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