Daniel, there was nothing in the terminal output..

I did notice that there was an update for Epiphany, but I don't think I
had it running during the update, I think this happened after... But I
never noticed the ephy-bookmarks.xml file in there before. Either way,
both files were 0 bytes, as well as the 'backup' files ephy-
bookmarks.xml.backup-LmhzJl.xml and bookmarks.rdf.backup-w5Qamk.rdf

-- 
Epiphany-browser bookmarks deleted when disk space runs out
https://launchpad.net/bugs/48604

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