Yeah I tried that, there's a few problems with that:
There's a lot of sub-script calling (set variables = flag number, CallSTD #) where the "Flag" logic is a variable. Example script file is the Hidden Item script (furniture overworlds) @ script_1241
scriptfile_1241: PPMax on Route 2
=== Script 131 ===
Offset: 4782 LockAll
Offset: 4784 SetVar2A 0x8000 53 - PP Max
Offset: 4790 SetVar2A 0x8001 1 - Quantity
Offset: 4796 SetVar2A 0x8002 2951 - Flag to Set
Offset: 4802 CallStd 2811 - Item giving script @ scriptfile_1238, givehiddenitem+sets flag, deactivates OWtile
Offset: 4806 WaitMoment
Offset: 4808 UnlockAll
Offset: 4810 End
NPRE's "dump" isn't functional so I have to scan all 1288~ scripts one at a time in NPRE. On top of that I have to account for the variable flag calling :\
The save files give me a general idea on what blocks of flags are used; large swathes of undetected usage with all save files indicate an unused set of flags. For a not-totally redone game, a few hundred flags should be sufficient for added content.