If some lines are blocked, it will put pressure on the rest of the irrigation system and can cause ponding or runoff of water. More serious blockage puts pressure on the discharge pump leading to extra wear and tear and eventual pump failure (normally just after the warranty has run out…).
To flush the lines, simply open the taps and run fresh water into the pump chamber at the end of the Wastewater Treatment System. This allows fresh water to pass through the lines, purging contaminants out the end of the lines. Some irrigation systems will have provision for connecting a hose, rather than putting water into the pump chamber.
All irrigation systems will have flushing points somewhere, normally at the end of the irrigation lines; you can learn more about this here: