@Erik Wooldridge Thank you for reaching out to us, As I understand you want to move from Azure AD Cloud sync to Azure AD Connect, you can follow this approach install/setup Azure AD Connect in staging mode, make sure all users/groups are in proper scope as per your requirements and verify the same in metaverse.
If the configuration matches as per your requirement, go ahead with the removal of Azure AD Cloud sync agent and move the Azure AD Connect from staging to production.
Let me know if you have any further questions, feel free to post back or we can connect offline discuss further as well ( you can reach me at by sending an email on azcommunity [at] microsoft [dot] com referencing this issue with a subject line "ATTN:Givary" and link to this post.
Please remember to "Accept Answer" if answer helped, so that others in the community facing similar issues can easily find the solution.