I do not know what to do about the shut-downs, but why are you needing to do multiple deletes of clients?
I only bring forward files from prior year when ready to work on or extend a client; so non-returning (ie ex-clients) do not clog up databases. Returns that have been completed are in the appropriate sections of databases and have acknowledgements attached; therefore not deleted.
We are not limited on how many clients we are allowed (even if you bought a software package that includes a preset amount of returns efiled/printed before PPR)
are you deleting from the module home base (1040, 1065, etc) or from the EF Home Base?
I delete some every year, but from the module home base. I bring all clients forward, then note the ones in house with the red Exclamation (info needed) tag... and use client status to segregate the completed ones, and ones still to do. but we each have our own dynamics on keeping track.