kontiki99:
I don't know what catagory your aircraft is so I don't know which FAR Part governs your aircraft, but I am constantly involved in producing STC products under Part 25, Transport Catagory Aircraft. In our world at least, a Flight Manual Supplement limitation can be removed but normally only through a configuration change. Removing such a limitation would require demonstrating to the FAA that the reason for the limitation has been resolved.
Typically that occurs in one of two ways. First, the STC for the offending equipment (the 3rd party STC, in your case) could be amended to resolve the condition that required the limitation. Second, some other configuration change may occur on the aircraft (another STC, a service bulletin, etc) which, while in the process of changing the aircraft configuration, resolved the condition that required the limitation.
In the few cases where we can remove a limitation due to configuration changes, it requires analysis, testing, drawing inspections, or some combination of the above to substantiate removing the limitation.
Without knowing the catagory, FAR Part, details of the limitation, and the existing aircraft configuration, I am unable to offer any more specific information. The earlier suggestion by Kwan to consult a DER with experience in the equipment that causes the limitation is an excellent idea.
debodine