The original BB controller could not make tool changes from a single file. But since you say you used to be able to do multiple tools in a single file on the BB controller you must have had one of the tool change routines installed that can be found on this forum. Like this one - but there are others.
Do you remember installing such a thing? Perhaps the firmware upgrade un installed it.
This is curious. Is it Carveco’s post that is telling you that? Have you updated Carveco or it’s post? Where do you see the warning message?