What kind of "falling appart" have you observed

What kind is irrelevant, it will change from case to case.

It is imminently possible - even likely - that the URTOS uses interrupt enable and disable to control some sequences - e.g. I can see many URTOSs that can not handle some interrupts during task switching. Then when you start to independently fiddle with interrupt enables and disables this whole scheme fall apart. Any URTOS I know of has, in the manual, very specific directions for writing and controlling ISRs. Also, it is very possible that some function of the URTOS is using the UART and get stuck when you try to control it outside the URTOS.

I wish I could say "stick the thing in your ICE and see what happens" but that would require that you had an ICE which you do not indicate. This is one of the situations where almost nothing but an ICE will help you.

The project you have is quite ambitious for making with limited tools.

One possibility would be to use s SILabs chip/board, there you get ICE capability for $99 - $149.

Erik