What are the .Lyx~ files that Lyx is saving near my normal files for? They don't seem to be temp files as these are marked #*.lyx#, and they don't go away.
What are the .lyx~ files for?
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For the reference of those who stumble across this page in future, like me, here's a more detailed answer from the lyx users' mailing archive.
Apparently, the *.lyx~ files are used to recover the file when a save fails. The #*.lyx# files are used to automatically backup the file every so many minutes. The latter are automatically deleted when the file is saved. The former are not.
They are files created by your editor. Traditionally files that end with a tilde are to be seen as backups of files with the same name but without the tilde. See the wikipedia page for an explanation.