If all the tables have the same structure, create a single table above the MERGE Storage. Truncate such a table will clear all the tables in the join.
True, I have a strange jamb on Server version: 5.7.16-log MySQL Community Server (GPL). After TRUNCATE, the SELECT above the table shows that there are no records, and SELECT from separate tables shows that the records are in place. And only after inserting at least one record into separate tables, it turns out that there are actually no records that were displayed ...
UPD: Ie after the TRUNCATE table you need to execute the FLUSH TABLE table .