Hi Philip,
The only way I can figure out for this to happen is if your operating system has removed the swap files before you write the projects, as part of an automatic cleanup of the /tmp directory. This is indeed very odd on Linux (should never happen as far as I know). Try setting PixInsight's swap directory to a different location; for example to a directory under your $HOME directory. Use EDIT > Global Preferences > Directories and Network > Swap Storage Directories, remove the default /tmp directory, add a different one, and execute the tool globally (F6).