Hi @George_H
As you rightfully say, QuickFile only supports one rate per period at the moment, so when it comes to submitting the return, it will need to be manually adjusted to account for the rate change.
Changing the rate on QuickFile half way through a VAT period would change it for the whole period.
One thing that may be of interest, there was a post on the forums from another user who mentioned that HMRC may authorise use of the flat rate scheme for a longer period. I don’t have any details other than the ones in their post (linked below), but it may be worth checking that out with HMRC which could help save a bit of a headache