The way you launched the coop server - was it via FH2ServerLauncher.exe?
If yes, you encountered the following feature of vBF2 dedicated servers: the launcher does not explicitly say what layers of the selected maps to play. In that case the server chooses the layer based on the MaxPlayers setting. The problem is that for coop the MapPlayers upper limit is 32, no matter what the setting in the launcher says. So if a map has a 32 layer, you always get the 32 layer in coop, otherwise the server defaults to the 64 layer.
To circumvent this behavior, instead of using the launcher try running the fh2_w32ded.exe server via command line with your custom map list edited by hand, for example:
maplist.append pointe_du_hoc gpm_coop 64
An example of the command line:
Fh2_w32ded.exe +ai 1 +gameMode gamemode +config "@HOME@/ServerConfigs/_serverSettings.con" +mapList "<Path to your map list>" +modPath mods/fh2 +ignoreAsserts 1