Is the direction that they now only move in the same direction as they move when homing?

It may just be that the settings are all screwed until it completes a homing cycle correctly. e.g the machine thinks its in some stupid position, and will only move towards it's expected correct range. Maybe X thinks its at -1000 and knows its only allowed to be -500 to +500, so will only move +ve until it thinks it reaches -500.

First thing to try is disabling soft limits. That should prevent the system babysitting your positioning.