I would say generally not. Recent version of Outlook do a fairly good job, in my experience, of not using files associated with another MAPI profile and there's virtually no "bleed through" of settings between disparate MAPI profiles.
If you're concerned about interaction with existing MAPI profiles and Outlook data files you could opt to rename the registry key (HLCU\Software\Microsoft\Windows NT\CurrentVersion\Windows Messaging Subsystem\Profiles) and directory containing the files (the AppData folder you mentioned in your question) while you're troubleshooting.
Blowing away a large OST file (particularly in today's world of hosted Exchange where it might take hours or days to re-cache a large mailbox) seems like something that shouldn't be done lightly. Keep that in mind when you start nuking files in the Outlook AppData folder. Even with an the mailbox server on the LAN you might have a multi-gigabyte mailbox to re-cache when the problem could have been solved w/o deleting the OST file and creating the network traffic and resource utilization in the server infrastructure.