I wouldn’t think it would create clogging scenarios usually but the PID tune does allow the firmware to learn the relationship between power applied to the heater and when the thermistor registers temperature changes.
Since you’re getting clogging and after a few minutes that could be from heat creep and there’s always the possibility that it’s being over zealous on the temp since it’s applying heat, not seeing enough increase, applying more heat.
Worth a try since you’d normally want to do a PID tune when you change anything related to it.
For me I do a bed tune when I change plates, and an extruder tune when I change any of the extruder hardware (fans too). If I’m printing in a material where the part fans will be high enough out of the norm I’ll do one with the fan at the given speed (e.g. my dual 5010 fans anywhere about 80% will blow back to the heater block even with creative use of Kapton tape to stop drafts and a PID tune helps mitigate any issues there.