How much compatible is it to put a Proto E6 A Unit shell on a Proto E7 A Unit chassis? The E6 has that slightly longer nose than the E7, so could this cause some compatibility problems at the rounded front end area? As for the B Unit I don´t have any concerns that it won´t be compatible.
As for the truck frames: can they be easily taken off the trucks? I´m aksing this because I would need to do that as well, since the E7 is a UP engine and the E6 an ATSF engine. And I don´t wanna paint the E7 trucks silver if it´s not too difficult to take off the truck frames.
I have a Proto 2000 (Lifelike era) DCC E6 A/B set. I can’t comment on the body differences with other models.
I don’t know for sure if my version E6 and your E7 trucks are alike. On the E6 I recently got into substituting a new front truck and putting replacement axle gears on the rear one. I did remove and reinstall the 3 pieces outside the axle ends; i.e., the truck frame and the left and right brake assemblies. I first removed the geared axles w/wheels. First the two truck bottom covers are gently pried off with a screwdriver. It seems a bit abusive but they did not break their tabs or distort. Then the axles lift out. At that point the truck frame can be gently spread so its sideframe pin receivers are pulled from the truck body side and the frame can be twisted off. The brake assemblies have holes that go over the truck sideframe pins and sort of come with the truck frame. Like you I needed to use the old side frame as the old were silver and the truck replacement was black.
In reassembling I had a few moments where it seemed tricky to get things aligned and inserted and such. One clue is if the bottom cover plates are not going on right something is preventing that, like an axle not seated properly in its frame slots or in the sideframe journals. If you can move the axle sideways enough that the square bearing does not stay in its slot, something is amiss. Be aware of how it comes apart and when reassembling avoid what seems excessive pressure on anything to avoid, for instance, breaking the frame (I suppose that could happen).
Hope this helps (if the E7 truck is the same as the E6).

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The frames are the same, but the E6 has an extended front coupler pocket. No problem if you don’t mind using the covered pilot.
@ Paul: thanks for the detailled answer! Helped me a lot!
@ Dave: yeah, I plan to use the covered pilot anyway!
I´m planning to use the ATSF E6 A-B Unit on my Chief, which is made up of 11 Märklin cars (6 sleepers, 2 baggages, 1 diner, 1 observation & 1 dormitory lounge (customized out of a sleeper)). Their trucks and floors are plastic but their carbody/shell is aluminium, and all cars feature interiors, passenger figures, interior lights and even brass venetian blinds. The electrical pick-up and dcc decoder for the interior lights is in the observation car and all cars are connected with electrical couplers to avoid friction. I really don´t know if that A Unit will have enough traction force to pull that train but I really hope it will! Gotta take the risk and buy it and try it out…