I've been through a couple of SharePoint Online migrations now, and I keep running into the same set of challenges regardless of how well I plan upfront. Wanted to share these and see if others have found better ways to deal with them.

Permissions are probably the biggest headache. Sites that have grown organically over the years often end up with broken inheritance, unique permissions on random folders, and access granted to people who've long since left the team. None of this maps over cleanly to a new site, and sorting it out manually takes far longer than the actual content transfer.

Metadata and content types come in a close second. If the destination site doesn't have identical content types and columns already set up, metadata either gets dropped or mismatched during migration, which causes a mess for anyone relying on filtered views or search.

Version history is another common pain point. A lot of native methods either ignore it entirely or only bring over the current version, which isn't great if your organization needs an audit trail or has compliance requirements.

Lastly, downtime and syncing during a phased migration can get tricky, especially when users are still actively working in the source site while migration is underway.

Because of these recurring issues, I've moved toward using a dedicated tool rather than manual methods. The DRS Softech Tenant-to-Tenant Migration Tool has handled permissions, metadata, and versioning far more reliably in my experience, along with better tracking throughout the process.