Diagnostics
Problem
When changing an existing adapter connection CON1 configured as an MS JDBC adapter to an MS ODBC adapter and keeping the same name CON1, any data retrieval from the Master File configured for this connection will fail.
Solution
When you configure an adapter and generate a Master File, the suffix is added to each Master File that is created for this adapter. If you change from JDBC to ODBC in an SQL Server, it is like changing the adapter from Oracle to DB2.
The choice is either to run a script to change the suffixes in all of the Master Files (This is possible with any text editor like TextPad or Note++), or you will need to regenerate all of the Master Files which can be done in mass or as many as possible in a single pass.
There is a slight chance there is a difference in data mappings between JDBC and ODBC, but no significant. Regenerating the Master Files is the safest way to go.