Happens at least with .ods & .odg => not specific to calc.
mkdir -p /tmp/a/b
create a file, ex with calc, as /tmp/a/c1.ods
mv /tmp/a/c1.ods /tmp/a/b
with file manager, open c1.ods in /tmp/a/b
menu -> Save As... as c2.ods
; you get /tmp/a/b/c2.ods (that's ok)
; but lets repeat without closing libreoffice:
menu -> Save As... as c3.ods
; you suprisingly get /tmp/a/c3.ods
; instead of expected /tmp/a/b/c3.ods
; note: before saving, you can see that libreoffice will now use /tmp/a/, if you pay attention to the path.
=> libreoffice changed saving path without explicitely notifying the user.
Then it is easy to loose updated files because they got saved into a different/old path.
The old path could even be the one you used for a totally different file, and thus saving in a location you will not think of looking at.
Is it possible to have libreoffice saving, by default, in same path as the file that was opened ?