I believe the addition of the launchkey should have zero chance of impacting digitone saves. Have you had an opportunity to look through the digitone bug reports thread to see if anyone else had a similar issue? probably a good next logical step is to browse through and see if there’s a similar issue described.
I guess the only other option is to open an additional ticket, but it couldn’t hurt to reload the OS over din midi with sysex first. Fresh start sounds like a problem with the machine to me though, they’ll decide for themselves but someone at support might decide to replace the unit if it has to come back again and is under the 3 year warranty still.