Its been a long time since I crossed the border by canoe, so I looked to see what kind of permits I was getting.  Going into Quetico thru Prairie Portage, I had a Moose Lake BWCA entry - just one, an overnight permit that had an entry date same as Day 1 for Quetico, and exit date for Day Last. Through Cache Bay, had a BWCA permit via Saganaga, and it was set up the same way, as an overnight permit with Day 1 as entry date and Day last as exit. So apparently that is how they issued the permits and make an exception to the no in and out rule for gong and coming to/from Quetico ?  or maybe it was Don't Ask Don't Tell ?  My last trip was in 94 - one way from Beaverhouse to Prairie Portage to Moose Lake - that one was set up by an outfitter, and the BWCA permit was for Entry 71 - Entry from Canada, and strangely, it also was an overnight permit with entry date being the same day we went in to Beaverhouse and exit day being Day Last even though we did not do anything more than paddle from PP to Moose Lake landing.

I'm thinking that there is no quota or limit to those Entry from Canada permits or it would be a logistical nightmare - so I'd think you could always get a day-use for Moose Lake, as an entry, and then the 71 for the time you wanted to come back across the border ?

at the bottom of that brochure I linked to, there are phone numbers for the BWCA ranger stations - I'd just give them a call and ask them how to go about it.  For me, I'd get the permits, but the boat registration thing would be a deal breaker today - back then, we always had my Dad's Grummans registered in NY for use with a motor (actually got checked on that by a MN Game Warden (or whatever he was) in a boat.