I have a REPLACE query running for a few days now on a few MyISAM tables, the largest having 20+million records. I need it to stop.

It is, basically:

REPLACE INTO really_large_table (a,b,c,d) 
SELECT e,f,g,h FROM 
big_table INNER JOIN huge_table ON
big_table.x LIKE CONCAT('%', huge_table.y, '%');

I need to KILL it, and I am worried that I may corrupt really_large_table.

Because the sub-query itself takes a significant amount of time, the REPLACEing probably occurs (relatively) infrequently; if this is true, does this make it less likely for the data to become corrupted?

For the curious, here is the SO question asked about the query I am trying to kill.