We have now resolved this, it was an issue with the app prefix id.

We have resolved this. we are still using the old format which according to the documentation allows us to specify the app identifier using either the TeamID or the App Prefix ID. we have always used the teamID. The new format only allows the use of the App Prefix ID, but it turns out that after some update recently (i suspect it might have been 17.3 based on some data we have) even the old format won't work unless the App Prefix ID is used. we changed the App-association file to use the App Prefix ID instead and it started working.