Something happened to some system file in the phone The only thing root checker does is request root access. If it gets it, it reports that the phone is rooted. If not, it reports that the phone isn't rooted. And root access depends on the presence of a single file being in the phone. Some apps do checks on other parts of the system and won't run if, say, the phone doesn't pass the SafetyNet check, which a rooted phone can, but some phones with compromised security (even some viruses) won't.
Try updating the app. If you're running one of the newer versions of Android, things have changed, and an older app may see one of them as a security problem.
If it still doesn't fix it, there is a pretty involved process you can go through. You install TWRP, so you can make a complete backup. Then you reflash the stock ROM, so you know that you have an unrooted/certified phone. (If it doesn't work at that point, and it's a fairly new phone [say, within the last 2 years], that's their fault. [I changed banks when my old bank wouldn't update their app so that I could deposit checks with my phone - on a brand new Pixel 2. They kept saying that they were "working on it". I was "working" too, traveling to the bank branch, so pay me for that - or lose my considerable account.]) If it works at that point, restore the TWRP backup and the banking app should still work. (A lot of work, but software debugging is like PTSD - one thing at a time.)