Short answer
HubSpot's KB: if the reply setting is on, a reply unenrolls the contact, but in most cases out-of-office replies will not, because the tool detects certain automated replies from the server's response code. A known exception: Gmail out-of-office replies sent to Outlook inboxes aren't recognized, so those contacts are unenrolled. Unenrolling stops future steps but does not undo emails already sent.
1. Sequences
My demo portal's sequences tool.
2. After a big send
Filter recently unenrolled contacts and re-enroll any that only sent an auto-reply.
3. Related
Sequence settings and unenrollment.