Try this. From a command prompt, find the names of all installed flatpak apps with:
Grab the full name of the flatpack version of Sigil (should be the second column). It might be something similar to com.sigil-ebook.Sigil.
Using that full name (case sensitive), try to run it from the command prompt with:
Code:
flatpak run <insert flatpack sigil full name here (without the angle brackets)>
See if that gives you any further detail.