When I take an armature that is rotated and use ‘apply size/rotation’, or even If I rotate any bone in editmode, it no longer is usable with the actions, they are expecting the original rotation. Any solution for this? Also sometimes I want to move action from 1 armature to another and same problem.
Yes, that’s expected behavior; the edit position of all bones (rest position) is the reference position for the Object (Armature) and each Bone when posed (much like Shapes have a Basis shape against which all others are calculated). That Rest Position contains data like Origin (of the Object), the Bone Relationships ( connections to neighbors, Local position relative to the Object Center, Scale and Local Rotation) and Roll Angle (the Global degree of rotation on the Y-Axis relative to the Root Bone [first bone added] which is relative to the Origin). Any of Ctrl-A, Ctrl-N (in Edit mode) and Alt-O will (possibly) break those relationships and the Ipos will then give a different translation to the one they were keyed in. Make it a habit to always do Ctrl-N and Ctrl-A before you start keyframing.