Can I reset the ibdata1 and ib_logfile files when innodb_file_per_table is already in place
You cannot (or, you can, but with pain &amp; risk).

For the ib_logfile[01] - you needn't worry: these are cyclic files, so your info will eventually be overwritten (and if you want to rush it, why don't you invoke a gazillion UPDATE foo SET bar=1 WHERE id=1 on some dummy foo table?

But the ibdata file cannot just be dropped.
Nevertheless you should (no guarantees held) be able to overwrite the file at those particular positions where you find your sensitive data. If you can identify all of them - overwrite them with spaces/whatever (say these are credit card numbers -- overwrite with "0"s).

I wrote on how you can use a replicate to convert all your tables to MyISAM (Assuming no foreign keys), restart, throw away your ibdata file, convert all back to innodb, get on with your life. It's a lengthy process as well. See: Getting rid of huge ibdata file, no dump required