I notice a reference to work on GP initial settings in the v3.5beta release notes, so perhaps this one has been fixed but I don’t think it has…
If a GP’s initial value is altered in the Editor, this change is not picked up by Refresh Counters. Perhaps there is a conflict here, since for an in-progress game, you would not want the current value of a GP to be over-ridden. Yet, for Scenario files, you would normally want the GP initial value to be updated by Refresh Counters.
A simple Checkbox in the Refresh Counters panel would fix the issue for module & scenario writers. To comprehensively fix the issue, to my mind, the vassal engine would need to keep track of whether a GP has been explicitly set during a game in order for Refresh Counters to be able to decide whether it should apply the new initial value or not… so that might not be viable and this issue would need to be borne in mind by module developers who might be using Refresh Counters to apply changes to an in-progress game.
A workaround is to temporarily change the name(s) of the GPs where the initial value is critical, then do Refresh Counters on the scenario file; finally, restore the correct GP names and repeat the Refresh Counter operation. However, this will become impractical ad the number of GPs and scenario files increases.