Yes, any sort of zoning or intra-zone "cutscene" transportation freezes statuses (using a conflux is considered the latter, but ONLY for when you're actually teleporting, not while you're in the menus choosing where to go) for a few seconds while in transit. This requires continuous, focused effort though, and at best will only serve to maybe double the length of a brew, and that's assuming you don't actually use any of it to fight anything.
Instead of trying to make a brew work over consecutive fights, you should rather try to gain the power to be able to beat stuff easily without needing one at all. Adoulin has made this pretty simple.
The only Abyssea NM that could still really use one nowadays is Rani, simply because despite our increased power she's still got nearly everything that can make an Abyssea NM annoying (damage absorption, having to fight mostly buffless except for probably Counterstance because otherwise she will just steal them via melee attacks, maybe about tied with Raja for having the most HP, power/defense increases when her HP gets lower, access to Meteor, stronger nukes, and charmga when her HP gets lower... the list probably goes on a bit further). Even if you don't necessarily need the brew to win, using one drastically shortens the fight and is particularly helpful if you're trying to get through multiple pops in a single 22:00-6:00 window for Epona's rings.