Hi @amega,
Thanks for coming here today, and sorry to hear about that strange, never-heard-before case you’re faced with.
Actually, based on how WordPress works, the File Manager plugin does not build up any files or data in your database, but it only allows you the access to your website’s files and data.
So, I am sure there must be a different source for this issue, but you can reach our tech team to try and help you investigate it here:
ninjateam.org/support
Regards,
Bruce