by Ken Task.
Moodle updates/upgrades seldom touch moodledata/filedir/ nor the tables related to files uploaded to moodle.
Suggest running the following query on DB:
select * from `mdl_files` where `component` like "%scorm%" and filename like '%.zip';
which should find the zip of the SCORM uploaded and it's location in sea of files moodledata/filedir/ as well as context and userid.
It is my understanding that, the only time one would loose all references to SCORM files might be if the SCORM's were remotely hosted or the links to them were pointed to a file system outside of moodledata/filedir/
'SoS', Ken