How can I fix my paper bag floor?

You can buy polyurethane that have a colour built in. That may be an option. Once you have sealed the bags the stain will not absorb the stain.

Only way to remove polyurethane is by sanding or a chemical stripper but both will affect the paper. Best solution I have is to roughen the poly surface with drywall screen mesh sandpaper or a 3M green scrubby. Not a kitchen scrubby because it is too rough. Wipe down the floor well with a damp cloth. Then use gel stain to give it color. Let it dry and polyurethane over it.

the poly will more than likely have to be removed first or else you could use stain over the poly now and then when it dries add another coat of poly

Redo your paperbag floor over the poly then stain and poly over. Do a light sanding of the existing poly before laying new paperbag floor. I have done paperbag floors so I know this will be your best outcome. Live and learn - but worth the redo. : )

Here are all kinds of tutorials and success and failure stories from Hometalkers about paper bag flooring: https://www.hometalk.com/search/posts/?filter=paper%20bag%20flooring