I've recently been giving EV a once over and have found something I'm not sure what to do about.
Checking the queues, I can see a legacy Exchange server that was removed some time ago still has 11,000 messages in the A1 queue and some in other queues. All the mailboxes concerned would have been migrated and processed from a different server in the meantime.
Is there anything I can do with these? Or should I just delete them? I'm hoping since they weren't processed fully previously that not data would be lost since it wouldn't have deleted the original item.
As the target is removed, your only option is to purge the queue. In the Administration guide is a description of what each MSMQ is doing. A3 and A5 can be purged without issues (these are the 'mailboxes to process', A3 manual run, A5 scheduled run).
A1 is 'pending items to update' and 'failed operations'. Due to the target not being available anymore, purge. Users might have 'pending archiving' items in their mailbox due to this.
If you want to be sure, talk to support.
A1 queue is for post processing items converting the items from pending shortcut to a regular Enterprise Vault shortcut. Since the target Exchange server no longer exists this post processing of the items will never occur. I'm expecting that some of your users probably have pending shortcuts in their mailboxes.
What you can do is revert the pending shortcuts back to regular messages by following the technote https://www.veritas.com/support/en_US/article.000028261, using solution #2. Be sure to run this after you all your current A1 queue's are at 0 so you do not revert the new pending items. Once the items are reverted back run archiving task to have these items archived again from the current Exchange server.
And then you can just delete the MSMQ pointing to the old Exchange server.
If you have any questions, please open a case with support where they would be happy to assist.