Hey Dajo,
A couple of comments.
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If you can import e57 files but are having problems with model calculation, then you may have an issue with Minimum Distance Between Points or Vertices. Not sure if you’ve looked into that already. If not, there are some posts here that will help.
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If you haven’t already, try to get a trial licence for Cyclone or Register 360 from Leica to see if that would work for you. I’ve used Reg360 and it’s much simpler and straight forward than full Cyclone. I was able to export useful .ptx files but not .e57 from that.
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Exporting registered .e57 files from Recap has worked fine for me before. What I’ve done is register everything in Recap, then export as one .e57. I’ve also seen some mentions here about having to export each scan as a separate .e57. Maybe try that and see what works for you. But overall Recap should work.
I really liked Register 360 (over Recap). It’s pretty basic, but works well. Especially if you don’t have a ton of scans.