Yes you can however there are some considerations.
1. To update a system variable you have to retrieve the entire variable, modify it and then save it back.
2. Doing this update is not thread-safe so you have to use "First in First out" on the channel and this can have performance concerns.
I would suggest that you load the CSV into a database and in the channel, use SQL commands to delete the row. This doesn't require loading every record and is thread safe allowing you to process more than one message at a time. You can also import any new records into the database as you receive files and not have to merge them in.