@Maurice_Bakker thanks for your comment, great to know I'm not the only one! To mitigate this issue, I had to run a subsequent flow on all of the top level folders to change their content type back to the document set content type (in my case change content type from 'Folder' to 'Job').
On the majority of the document sets, it did then cascade the metadata down to the files beneath after the content type update, but it didn't work on all of them for some reason. In some cases I would check back after a few hours/days, and the metadata will have eventually cascaded, but for others (i.e. weeks, months on), it still hasn't cascaded.
If we could get the original problem sorted at the migration stage then this wouldn't be an issue, but with the metadata missing it has thrown off so much more of my policies/strategy that it isn't a viable method when using document sets.
