@rextended routing can be marked only in prerouting and output
For explanation how it works see this:
http://forum.mikrotik.com/t/v7-3-and-v7-3-1-stable-is-released/158530/87
The change was made to fix the problems marking VRF traffic with the mangle.
It was always not recommended to override mangle with routing rules, if you had this setup previously, then yes unfortunately you have a broken setup now.