Oliver, I've experienced similar type situations, and have corrected it by adding a second data source ( File > Manage > External Data Sources ), and switching the TO to that second source, keeping the same TO name, and then saving.
It's inconvenient, but filemaker seems to cache the ESS connection settings and schema data on a deeper level.
The sync button will only pull the schema data from the source it's connected to, and I have previously proven in my testing that it caches the connection data in the relational graph, even if you change the ODBC DSN settings, and the data source information inside FM. The way around it was adding a second source, and changing all of the TOs.
Offhand, is your OLD data source still available while this is going on?
I will try that
In My schema I am trying to have only one TO link to each ESS table, and any extar ESS TO's based on the shadow table in FM rather than direc to the ESS table -- so I should only have to change teh TO once for each SQL table.
I did make some progress by syncing every Table before creating the new copy of the database, but still some TO's were misconfigured.
Your method will take longer (not much though) and if it proves 100% reliable that will be a relief.