Alright, I've got somewhere with reproducing this.

1. Ran the command replay forward & forced a dmp_cmds save at 000ad053 (the same date that Hopsi joined, though 9 ticks before due to some weirdness in the desync replaying stuff)
2. Started the game again with that new save (basically acting as if I'd joined the game at that point
3. dbg: [net] sync check: 000ad0ef; 00; mismatch expected {33188c8c, 1d7b69f5}, got {007a3060, 2361519c} & and differences in the save game just before (ad0e0)
4. using the zpipe & printhunk utilities, found the diff in the ad0e0 savegames (my generated one attached) - this pointed to a few bytes in the MAP2 chunk.

So, something in the map array that's using .m2 , presumably something that's changed since 1.9.x .
Probably.
dmp_cmds_086e2f4d_000ad0e0.zip

Hopsi Transport Train 1 is in two completely different positions in the two savegames.

I had a look at one of the differences in M2 and it looks like the PBS bits for rail (class 1).
The first difference in M6 looks like the PBS bit for stations (class 5).

The dump utility seems to give up at the start of the VEHS chunk for some reason.

The trains are also different lengths by 6 wagons. 6 wagons are left in the depot in the original save.
That seems a bit suggestive of a problem with the _new_vehicle_id/CcBuildWagon mechanism...

Might be related to the build+refit feature for vehicles.

@frosch123 noted on IRC:

the GroupStatistics stuff in the build+refit looks fishy for sure
the OrderBackup in there may even cause a desync

I have no time left today to test this, but pretty sure this is capable of causing desync:
frosch123@871ca6d

Interestingly, getting a build and refit cost estimate re-arranges free wagons in the depot.
NormalizeTrainVehInDepot() is called to attach assorted free wagons to the temporary engine, and when the temporary engine is deleted the wagons are released in a single chain, which is a potentially different configuration.

I have no time left today to test this, but pretty sure this is capable of causing desync:
frosch123@871ca6d

The group statistics are also updated when the temporary engine is sold, this change makes the statistics go negative. This aspect seems OK as it is.

Interestingly, getting a build and refit cost estimate re-arranges free wagons in the depot.

I can reproduce this in 1.10.1 stable and in 2020-04-26 master nightly.

Estimate cost is not even necessary it seems. I can "move" the wagons just by selecting an engine in the list while a cargo filter is set.

Do I understand it correctly that to get that vehicle desync player needs to estimate build or refit cost in some special circumstances? If that's the case it may not be the main cause of most desyncs as many players seem to disconnect just by creating a company or shortly after.

19:44:33  <andythenorth> protocol error, connection closed
19:44:49  <andythenorth> do we have a desync log?
19:45:06  <_dp_> *** Player has left the game (wrong company in DoCommand)
19:45:09  <_dp_> o_O
19:45:12  <_dp_> was that you?
19:45:20  <andythenorth> yup
19:45:35  <andythenorth> triggers on 'New Company'

and some to even desync as spectators

<RedditServer1> 22:58:55> *** petrpletsvetr has joined
<RedditServer1> 22:58:58> 'petrpletsvetr' reported an error and is closing its connection (desync error)
<RedditServer1> 22:58:59> *** petrpletsvetr has left the game (desync error)

Oh, wow, I just got desynced myself while spectating and it put the game into the invalid state (same as in #6598). It appears to still be in the game but it's missing the client list and is not actually connected as seen in another game instance.
Although both server and client are modified in this case so can always be blamed on that I guess.

@frosch123 🎉 - reckon we’ll be seeing a point release for this any time soon?

I think that's quite likely, though we'll want to make sure that the problem has actually been fixed (or that there aren't any other problems like @ldpl is suggesting)

FWIW here how it looks from the player pov:

[Server #0] Player: but... what happened today...
[Server #0] Player: i have gone once...
[Server #0] Player: to return and i wanted to look: how much time is left to restart :-)
[Server #0] Player: and then:  i couldnt connect anymore
[Server #0] Player: i tried some 15 times or so
[Server #0] dP: what did it say when you couldn't connect?
[Server #0] Player: synchronisation error
[Server #0] dP: were you trying to connect to a company or as spectator?
[Server #0] Player: it said that after some 5 seconds or so
[Server #0] Player: both
[Server #0] Player: i tried to connect to the company first
[Server #0] Player: then as a spectator
[Server #0] Player: i was both times as "Player" then
[Server #0] Player: i mean, not both but 15 times
[Server #0] dP: so it just connected to the game normally and after a few seconds kicked you out with desync message?
[Server #0] Player: yes, seeemed so
[Server #0] dP: damn :(
[Server #0] dP: oh, and what os do you use?
[Server #0] Player: win7

So he was fine until he left the game himself and couldn't get back anymore.