anything in the transactions logs to indicate any issues (/usr/nsh/Transactions/logs/bldeploy-blah.log) ?
is there anything particular about the files compared to ones that do get deleted?
Nothing in particular. The log shows the item (the delete) as being processed.
And if you actually ssh to the server the files are still there? And they're not read-only or have some other security context applied to them that the others do not?
I'd say open up a ticket w/ support.