Same problem. Upgraded client to Focal, server is Bionic. Both have unison 2.48 
and I have the 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."

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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.

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