Once you’ve migrated a 3.x query to version 7.0, you can’t alter it anymore within a 3.x query designer, as a 7.0 query is not downward compatible.
(Even though you can still execute a migrated 7.0 query with a 3.x BEx Analyzer/Query designer, you aren’t able to alter it anymore)
OSS Note 962530 (NW04s: How to restrict access to Query Designer 2004s) explains the necessary steps to take to prevent unwanted migration of queries.