Hi Tommy,
welcome to the warm, wonderful, bug and flame free Atari section!

It
sounds to me like your Atari may simply need a service. I had similar problems a few years
ago with the file select routine showing all sorts of wrong or omitted data with
Notator.
It wasn't deleting the files, but it simply wouldn't show them when trying
to save, or worse, couldn't find the partition at all.
Barrie at Keychange
(www.keychange.co.uk -usual disclaimer as always) can sort you out on this, as he did with
my machines. Now everything works fine. I'll also point out that Barrie is the Cubase
expert par excellence, PLUS he does do data recovery services for those Nemesis striking
days......

Hope this helps,
Best wishes,
Dave.
--------------------
Lots of Ataris which keep on going, 12 Kurzweil 1000 modules, a bunch of hardware synths. Still recording to tape -the old ways are best.....