Change of RouterOS version not change the communication with mPCIe slot…
You should check if this lte module is still detected in System > Resources > USB .
I read you test many stuff but first I hope you write to support@mikrotik.com because you should have see still both devices.
I know only that LTE-US + LTE6 OR 2x LTE-US cannot work together by USB EndPoint limitation describe here: http://forum.mikrotik.com/t/tips-ltap-not-mini/141186/1