best bet is to contact Squarp via contact page and they can check your project.
I hightly doubt any ‘action’ caused the tracks to ‘disappear’ e.g. other projects/sysex.
only action I could think externally influencing a project would be related to sdcard itself… e.g. a failure on the card, or manually deleting overwritting files etc.
anyway, all this I suspect is pure speculation… so we should move on 
lets have a few facts… that might prove interesting/useful about whats stored on the sdcard.
BACKUP folder on sdcard
there is a backup folder on the sdcard.
each time you save the project it moves last project to this directory.
so we have ONE version of each project in the backup
implication : important note
if you notice your project is ‘wrong’ NEVER save it … you will destroy your working backup
I think the intention behind this is simple.
your project is working lovely.
you save it - all seems ok
the next day (or whenever) you come back, its screwed.
you can go to the backup to pull back the last successful save
(we know it was successful, as you’d previously loaded it)
notes:
- you will lose the last ‘sessions’ work. (of course!)
- this might not help if the sdcard failed.
- this is done ( I believe) as a move, so should not be prone to failure.
- if you delete a project the backup is not deleted
what is a project?
lets consider your failure in terms of how a project is stored by the pyramid
a project is a folder containing
- a core.pyr file - meta data about the project
- a midi file per track - holding midi events
so this means if you go look at your sdcard you can see if the midi track data is gone or if its just the meta data (core.pyr) is incorrect.
(my suspicion is you’ll fine the midi files are still there)
Core.pyr,
actually talked about this a little in this thread
this file details all the track layouts, fx used …everything that is not midi event data.
the core.pyr file is actually a text file , so you can view it
(make sure you COPY it to view it, if you accidentally make a change it will very likely become unreadable)
its not a particularly complex file format, even without knowing it, you should be able to see if your ‘tracks’ still exist in it or not… and what state they are in.
so from all of this you can determine
a) has the midi data been deleted
b) does the core.pyr still have entries for tracks.
hopefully, this should give you some info…
and is also why I suggest contacting Squarp, as if they see your project, they will likely be able to
a) determine if there is a bug in loading project
b) if something is corrupt, determine what is salvagable.