Transition to innodb_file_per_table for 30+ databases Currently I have a MySQL Server with innodb_file_per_table = 0
Based on a number of factors, it seems to make sense for me to change that to innodb_file_per_table = 1
I understand that to make this all work I need to

Use mysqldump to export all databases into individual files
Shutdown mysql
Change the innodb_file_per_table setting
Restart mysql
Import each database

Question is, can I do the following
Day #1

Shutdown mysql
Change the innodb_file_per_table setting
Restart mysql
Export some databases
Import those databases back into mysql

Day #2

Export some databases
Import those databases back into mysql

Until I've exported an re-imported all of the databases?
I'm assuming that during the transition some databases will continue to use the ibdata1 file while the exported and re-imported database will use their own datastores.  Will having a mix of datastores cause issues or am I OK doing a phased transition?
I honestly wouldn't bother unless you have a specific problem you are solving.
Its possible to do simpler with:

Shutdown
change setting innodb_file_per_table = 1
start
ALTER TABLE xxx FORCE for each table