It sounds like when the script runs to alter the alarm property the UDT instance member tag considers the override on the whole alarm.
The simplest way to remove an override is in the tag editor using the green dot.
There is discussion of scripting to remove overrides on UDTs mentioned in this thread, but it may not apply to your scenario: Is it possible to remove overrides on alarm properties in UDT instances thru scripting? - #2 by jlandwerlen