From what I can tell the SH4 engine will crash whenever a reference is not resolved. Or in programmer terms, they never put try / catch blocks around the referencing code.
Now, with thousands of items all with their own id's and references between them. Once you start editing files it's going to become problematic for your savegames.
Or in plain words, it's really easy to **** up your installation if you mess around with cfg files. Just make 1 mistake and the game will BSOD at some point.
From my experience with this engine, unless you're 1000% sure what you're doing, it's perhaps better not to change anything in the game while you're playing. Or in a way, not even the "install in port" mentality is always safe.
Excluded are of course textures, sounds etc, which are always loaded on the fly, and can be installed even while the game is running.
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