I'm not quite sure what you're after, but tricks like this sometimes work:

1. separate the parts in the modeler,

2. counter-rotate the relevant part and re-save only that part as OBJ;

3. Use UVmapper on that OBJ and save the result;

4. Bring that mapped OBJ back into the modeler and re-assemble it with

the other part;

5. Don't let UVmapper alter that part again after it's re-assembled.

 

By counter-rotate, I mean turn the part CW in this step if you want the UV map to end up as CCW from where it originally was.

 

Got an aspirin?

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