We use to clean/flush the HPLC systems every 6 months (or more frequently if there are problems due to contamination).
Firstly, we flush the system with hot water (HPLC grade) and then with IPA.
Flushing the system with IPA can be done during the night at low flow rates (0.2-0.3 mL/min).
Finally, we flush it with water.
Mostly, this is only time-fixed procedure, that we are repeating on every 6th month, but cleaning of the system/column after every analysis is common every-day procedure.
Recently, I have been told that 0.1% TFA in water is a good solution for cleaning the detector cell and tubings.
Best regards