Litter problem (vent)

hi yall im just here to vent a little about a major problem with my bunnies. they usually stay in their large pen whenever im at work and in that pen is covered in jute/cotton mats. I usually sweeped their poop off of it and for a couple of weeks i did not lift the mats to sweep under them due to thinking it wasn't necessary. that was a horrendous mistake and I discovered they have been peeing on the mats. the main reason I never noticed is because the mats where dark colored and their pee blended into the already existing stains that i thought no longer smelled due to washing it. another factor is that I have a very poor sense of smell so I couldn't smell the pee that built up in the mat. i only knew smthin was up when my dad complained abt the smell and there is where i discovered it. so their litter box habits is broken completely and I started the retraining process. I feel like im a terrible bun mom for this as they absolutely dispise the smaller space they now are in.

my floors are ruined and I'll have to rip up the vinyl flooring and replace them because i do not know if im able to permanently erase the scent and restore them. i have a night shift job and i feel horrible now that theyre stuck in that small space for hours while im at work and sleeping. their routine and space is now ruined and I know they hate me for it. I wish I had more time to spend with them during the retraining process but I can't because of my job. i dont have anyone reliable to watch their habits so I don't even know if leaving them alone will even help since I won't be there to immediately clean up accidents.

this is not their fault and i am not mad at them. this is my fault and i shouldve done better.

Edit: also one more thing I should add- they have a litter box house- would it make it easier to remove that from their space and just keep the litter box by itself in the pen? Any advice would help thank you!