So I also found a workaround that works for me so far. It is also
downgrading to the bionic versions.

First of all, I downloaded the packages from bionic and installed them
manually (only unison and unison-all, though) as suggested by Sebastien
Koechlin and Helge Meinhard said. Then, I created a file to pin it to
that version so it will not get upgraded, i.e., in
/etc/apt/preferences.d/unison I have:

    Package: unison
    Pin: version 2.48.4-1ubuntu1
    Pin-Priority: 1000
    
    Package: unison-all
    Pin: version 2.48+2
    Pin-Priority: 1000


The other problem is that unison does not like to use the old archive files. 
You can try running unison with the `-ignorearchives` flag. If unison runs 
then, you have to remove the old archive file.

If you have only one archive, you can just delete your ~/.unison directory and 
then run unison afterwards without any flags and it should be fine.
If you have more archives and you do not want to rebuild them all, you have to 
find the proper file.
I did this in a stupid way by copying them out one-by-one (both the arXXX and 
the fpXXX).
The, I check if unison still reports an error and if so, it was the wrong 
archive and I copy it back.
If I found the correct archive, I just stop.
Maybe there is somebody who knows a flag which can tell you the archive file 
directly.

-- 
You received this bug notification because you are a member of Debian
OCaml Maintainers, which is subscribed to unison in Ubuntu.
https://bugs.launchpad.net/bugs/1868502

Title:
  Synchronization with earlier Ubuntu versions or a recent Debian
  version fails

Status in unison package in Ubuntu:
  Confirmed

Bug description:
  Any synchronization I want to do with my server (Debian buster) fails
  with the following message:

  > Fatal error: Server: Fatal error during unmarshaling (input_value: 
ill-formed message),
  > possibly because client and server have been compiled with 
differentversions of the OCaml compiler.

  Indeed, buster uses OCaml 4.05.0, focal uses 4.08.1. eoan used 4.05.0,
  as did the prior versions, including bionic, which all still
  synchronize fine. The current Windows version also synchronizes with
  that version.

  Although intentionally using an old software version for compatibility
  is not a good thing, in this case it might be necessary. The whole
  point of unison is its interoperability.

To manage notifications about this bug go to:
https://bugs.launchpad.net/ubuntu/+source/unison/+bug/1868502/+subscriptions

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