URGENT! Can't fix SU binaries via flash or flash TWRP?

So there's an issue I've been having and it's really been starting to bug me. I've got a half broken root which wont let me install, remove or do anything with root because of missing SuperSU binaries even after using almost all methods out there. I learnt of a way to do it by flashing the recovery with the SuperSU zip file which will fix root and install the latest version but there's a big issue, I can't flash the zip because recovery mode only gives me the option of doing it by SD which my phone doesn't have. It's only on internal storage. So I tried to flash TWRP like twice but the stock rom keeps replacing it and I have no way of getting around it. Is there anyone who can help with this?