I've set up the default jira (server) incoming mail service and set up the mail handler to create issues.
It is correctly set up as imap and not accidentally set up as pop.
Same behaviour on outlook.com and also office365.com domains.
The jira documentation explicitly states that it won't delete the emails but it is.
If JIRA successfully processes a message, JIRA deletes the message from your mail account (on a POP) or file system (i.e. for file system messages). On an IMAP mail server processed messages are not deleted but marked as read.