Ring and Loop based cutting

How about trying something like I described in this thread a while ago

You could potentially create some fairly complex ‘cutter shapes’ out of primitives using booleans - and then use them with modifiers to cut out the parts you want.

If you models are single colour - you might actually be to save the modified STLs and then reload them back in.

Failing that I would probably use Fusion 360 - although it is pretty slow for this sort of thing.

Blender is better for editing meshes - but then you might end up with a lot of trouble getting rid of non manifold issues.

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