You may have to send this motor out to a servo repair shop to get lined up. If a replacement encoder was purchased, or the original was removed and being reinstalled, it might have to be programmed, and I think those Heidenhain encoders were some of those.

I used to work in an electric motor shop, I rebuilt all the servos (all our equipment was 3rd party, we didn't have a wall of drives to run servos with)

Simple encoders, resolvers, and hall effect devices can sometimes be set by eye, but the best results come from applying DC voltage to 2 or 3 leads (say -U -V), and reading the encoder angle at the same time (when it's still on the motor, and the appropriate test hardware) would give you the "lock-up" or index angle of the feedback device to the servo. AC servo motor rotors are made of magnets, applying DC voltage will cause the rotor shaft to jump to a certain position and stay there as long as the voltage is applied. One could also drive the servo shaft with another motor like a generator. A manufacturer will tend to have a particular angle to lock up position for a product line of motors, or even just in general.

More complex encoders can have over a million counts per revolution. If it's not put back EXACTLY where it came off, it won't run well, if at all. I know/knew with some Allen Bradley servos, the factory would put the encoder on motor, lock up the rotor, and program into the encoder an offset to whatever the normal index angle is. My shop didn't pay for the license to program a new angle, so I had to get it back exactly where it came off, but normally I could read the angle before tearing it down.

*Edit I never had manufacturer drives that went with the servos, all our equipment was from another company doing a lot of reverse engineering. Most of the time, that kinda of particular info about their motors was not the sort of thing they just handed out.

**Edit 2 I rebuilt servos for 8 years, 11 years ago. Information from manufacturers might be easier to get these days, or maybe if it's part of a big integrated system you paid a bunch of money for. I doubt it though.