I'm glad that you were able to resolve your issue and thank you for posting your solution so that others experiencing the same thing can easily reference this! Since the Microsoft Q&A community has a policy that "The question author cannot accept their own answer. They can only accept answers by others ", I'll repost your solution in case you'd like to accept the answer.
Issue:
I have created Linked Services in the Data Factory using both the Dynamics 365 and Dataverse connector. I then created a dataset and copy pipeline to export all the columns to an Azure SQL DB. When I compared the extracted columns landing in the SQL DB to columns I can see for the table using Power Query I noticed a few columns I need for filtering purposes where no visible. So using the same linked service, specifically the dynamics 365 at this point, I change the copy activity to a dataflow. The columns where then visible and were created in the destination SQL DB. However, no data was tranferred, just the column name although other columns are populated. There is definitely data in the columns as I can see it in power query, I am comparing the same Dynamics environments and can't understand why I can see the column but no data is present.
Solution:
Re-checked the service principal security setting in dynamics and made sure it had the correct dpeartement etc. it is working fine now.
If I missed anything please let me know and I'd be happy to add it to my answer, or feel free to comment below with any additional information.
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