Thanks for taking a look. Your thoughts on what could have caused this made me think that this happened by mistake. My last backup was onto a new USB drive and I did it manually. In light of your comments its possible I moved the Sigil files instead of copying them i.e. cut and paste instead of copy and paste!
I'll restore the preferences folder which should correct the problem.
This just goes to show the importance of backing up your files.
Thanks again for the help.