I did (the shame), delete all files when deleting a temp FTP account (which had root access, note to self, never do that again). Just for me, our backup files that Site5 does daily just had to be corrupted (which they amazingly fixed after a month).
In the meantime, I installed the latest version of Blesta to continue operations, and the amazing team at Site5 has fully restored the old Blesta version (2.5.4) allowing us to export the database.
I tried running a import to the latest version of blesta 3.2.2 but had the following error message
SQLSTATE[HY093]: Invalid parameter number: number of bound variables does not match number of tokens
Question: should I start a new thread, or just continue here?