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Replace datasource, as you seemed to have discovered, really only has an affinity with the single datasource you are trying replace be it a primary or secondary. There isn't a way in the product right now for us to guess or let a user define that a federated connection (xDB join) is an equivalence of a number of blended data sources.
I may be over simplifying this but you could potentially take a more targeted approach to your existing workbooks, one that I took with my own internal workbooks here at Tableau. I went through my workbooks and found the cases where I had worksheets or dashboards that 1) I deemed too slow and 2) used blending. From there, I started experimenting with whether or not switch to a xDB join for my blends helped the performance. If it did, I put in the work to rebuild it. If not, I let it be.
Functionally, there are obviously a lot of differences between blending and xDB joins underneath the UI, but so long as it gets the results you need to see and within an acceptable amount of time, I wouldn't suggest you worry about creating all your work again. Even as you move forward, I would be sure to keep utilizing both scenarios. Sometimes xDB will be faster than blending and other times the reverse will hold.
I hope this helps a bit.
Just to be clear - are you replacing blending with xDB?
If yes - have you tried "replace references" for individual fields?
If you have sheets with blended datasources I'd just join secondary by adding it as new connection to primary. Yes, you'd have to recreate calculations from that secondary datasource in your xDB. Unfortunately, there's no better way at the moment.