1) Dump query result to SQL file in location A. Using the DBs dump tool is prefered.
2) Add SQL header (Create table ...) and footer (end transaction; create indexes)
2) Rsync with old file in location B.
3) Use DB B (un)dump tool into a temporary table.
4) Do a transaction on DB B: zap old table, rename temporary table.
This way minimizes network traffic and rsync does the INSERT/DELETE/UPDATE queries job. It becomes inefficient in step 3 if the file size is too large (several dozens of megabytes).
How many records are involved and which databases?
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