Unable to remove malware, even after factory reset and system flash. Sony Xperia 1 IV, XQ-CT72

I had a rooted phone, in which I misclicked an apk and installed it. Almost immediately I uninstalled it and disabled the network (I also had afwall and netguard enabled). However it was too late. I got a ~100's of 0kb system apps without icons. I re-flashed the phone with fresh stock firmware and factory reset it, however the broken system apps (and likely the malware) are still there. Does anyone have suggestions on what can be done to fix this? Or any knowledge of similar malware? Some antivirus I could use, or maybe something stronger than a system flash? Thanks in advance. Picture after factory reset and flash.