Have you manually changed the classification number for your regions?
I ran into a similar issue when playing around with the AI driven classification.
If you manually create a region it inherits the classification number from the source region.
So, although you may have two different region names, they might have the same classification number and that might be the reason why they get combined again.
That happens for instance if you export those regions into a LAS and reimport it. I was preparing a data set for the AI training, had two different regions, but hadn't changed the classification number.
Once I imported the LAS into my test project it did combine the regions into one again.