License for x86 version depends on software ID, which is computed from how disk identifies itself in system (I think model and serial number) and some random (probably) data on disk.
The former can be reason why your license was lost, if the virtual disk changed its identification for some reason. It happens for sure when you move it from one virtualization environment to another (e.g. VMware to VirtualBox). Upgrades of VM host could probably change it to, although normally it doesn’t happen.
Try to remember if you did some upgrades that could cause it. If so, try to install older version of virtualization software somewhere and see if RouterOS VM works correctly under it. If it does, examine how disk identifies itself in old and new version. If it differs, it could be possible to override it.
For example: http://forum.mikrotik.com/t/softid-has-changed-after-move-vhd-from-virtualbox-to-hyper-v/90794/1 (you’d need something like this for whatever you use)