Calibre has never
deleted a Library in all the years I have used it.
It has lost the LINKAGE (and other USER layer preferences) to alternate Libraries (names) and all I had to do was Switch/Create to reestablish the link (10-20 seconds of work)
Rogue A/V, User 'cleanup' (inc automated tools), drive failure and IGNORING the admonition to NOT have the ACTIVE (typically the ones in the Quick switch List) Library on a Network/cloud drive. Users have put the (actual) Library folder on the Desktop, then cleaned up
All these are USER /. system caused. NOT Calibre caused
I have TRASHED the Metadata doing BULK operations poorly
I have deleted BOOKS in error.
Even when you select 'Delete' on the Library icon menu, all it does is remove the LINK. It pops a message telling you to use the O/S if you really want it gone from your disk