Just as update, we got the 2,4 TB File to dedup, I tried a restore afterwards, it had "read errors". Some files worked (Guest files Restore) others didn't.
So bad idea using Dedup with Windows 2016 as it seems broken, at least for us.
I tested a smaller VM under 500 GB which seemed to work fine.
Will now keep using Windows 2012R2 and not using dedup, even I don't know how big files would perform with 2012R2 - never tested it on my own.
Probably 9.5 with ReFS is the better idea, after some Windows 2016 and Veeam Updates
Anyway wasoff topic but wanted to give feedback.
Probably splitting files will still come anytime in the future.