Hello @JenniferYeager
Thanks for posting this in the global Canvas Community. I apologize that no one has responded to this yet. I am not sure if you have resolved this already, but I wanted to respond back to you on this.
From what I understand, cross-listing sections in Canvas should not impact the sync in anyway. Each section should have it's own unique SIS ID, which is used to passback grades. This issue would usually stem from something occuring with the data sync that takes place, or even the configuration of the assignments. Each sis integration is a little bit different and will have certain requirements to properly sync to powerschool correctly. Further troubleshooting might be required to resolve the sync issue, if you are still seeing it. You should be able to contact your school's Canvas administrator to have them take a look at the issue and troubleshoot further. You can also try to contact canvas support to see if they can have their team look at the course and the sync data that is being sent over to Powerschool.
If you have the ability, you could try to run a "Remaster sync" in the course's grade sync area. This will attempt to resync and reconnect the course with Powerschool. If it detects an issue during the sync, it will list an error that Canvas support can usually cross reference.
In some case you might need to contact Powerschool to have them look into it further.
Hopefully this helps!
-Colton