@RonaldoMysqlDBA has a good article on how to Clean a MySQL INNODB storage engine. Basically, what he says is that it's not that easy on a live server.
However, as I was reading about innodb-undo-tablespace I noticed that they mentioned the option of setting up a new server with the desired settings and then link it to the live server as a slave.
(7) Deploy a new production instance using the ideal settings for these
options. Set it up as a slave server in a replication configuration,
or transfer data from an earlier production instance.
The replication will then make sure your new server has all the data. You should be able to set it all up this way and then stop your system for a few minutes while you change so the slave (with the desired settings) becomes the master. This can be a temporary solution and you'll be given opportunity to make needed changes to the first server's settings.
I haven't tried this myself. I usually go with the old school method of dumping the database and then installing it with the new correct settings. My suggestion above is a bit tricky but if you have no other option it might be worth trying.