By deafult CE APM try to recover "all" the metrics from sysview that you know you should recover.
Using the CE APM conficuracion file, Cross-Enterprise_APM_Dynamic.properties, you can enable or disable the collection of a certain category of metrics or define through regular expressions, to filter specific elements of a specific category.
The above will not prevent you from having metrics in gray in APM for metrics generated from Sysview, since this will depend on whether the metric generated in Sysview has persistence or not. Since sysview many alerts are generated that in APM you will see them active only while the condition is maintained, then they will turn to gray immediately, since sysview does not generate the metric when the alerted condition changes.
Alerts from each cics regions
In general, the gray metric disappears if the EMs involved are restarted.
Remember that Sysview, generate metrics by default and others that is necessary configurate to that is generate
It is not clear to me which components changed version, so check compatibility between
Sysview - CE APM - CA APM
My customer do upgrade Sysview to 14.1 release and is necessary do upgrade CE APM to the last versión and do upgrade EM collector, in my case to the 10.5.2 release.