Copy a Large INNODB table in MySQL

I have an INNODB table that's > 93 million rows. A lot of the data is considered "temp" data and is governed by an "is_active" flag of 1/0. When a user updates a form, new data is written with an "is_active=1" and the previous active records are updated to "is_active=0". We wanted to move the data to a new table to clean up and ran statement like... INSERT INTO tblNew (a, b, c) SELECT a, b, c FROM tblOld WHERE is_active=1 This ran overnight and when I looked in the morning I noticed there were a bunch of processes backed up in the SHOW PROCESS LIST so I did a KILL on the process on the ID, which started the ROLLBACK and brought the server down for another 10 hours... production box of course. I've been reading a lot on how you can try to repair, etc. and have been doing that all day, but I'm wondering if there's any kind of option I could have added to avoid the need for rollback on failure? Or is there a strategy commit or flush every X number of rows, etc. I was trying this... INSERT INTO tblNew (a, b, c) SELECT a, b, c FROM tblOld WHERE is_active=1 AND pkID > 0 AND pkID < 1000000 Where the pkID was the primary key. I would run it in groups of 550k - 1M and up the number range for PK each run. There's an index on the PK and on is_active, yet I noticed speeds increased each run from 30 seconds to over 5 minutes a run by time it was in the 20M range. Any idea why this would take longer each run when it's the same number of rows for the work? So 2 in summary, questions... 1) Can I do something to keep a huge rollback from happening if I stop the process? 2) Why did inserting the same number of items based on PK and indexed column take progressively longer per run?