My bike won't shift into the two smallest cogs in the rear when it is in the large chain ring up front.

When I connect it to e-tube, it "thinks" it is in the smallest cog. It shifts fine into the other cogs going up and back down aside from those bottom two cogs.

I have tried the crash recovery mode, and it shifts up, hits the largest cog and stops. When it hits that cog, it thinks it is 2 from the top.

The bike shop checked the derailleur hanger and it is straight and didn't need adjustment.

I adjusted the offset to +and -16 and the best I can get it is to one away from the bottom. But I don't think that is a reasonable solution.

I would like to just reset cog it thinks its in, but I can't seem to figure this out. The local shop has never seen this and tried everything they could think of, but they can't seem to get any farther than I have.

Edit: There was a comment about a spacer on the cassette. However, The bike is using the original cassette that has never been off the wheel, and the wheel came off the bike, and until the other day it shifted flawlessly.

Any help would be appreciated.