The app can erase the fault memory on every supported Yamaha four-stroke, from the FX140 of 2002 up to the current models, and it takes a few seconds. That makes it the most tempting button in the whole app and also the one most often pressed too early. A cleared memory feels like progress. It rarely is.
Write it down before anything else
Once the entries are gone, so is the clue that told you which circuit to look at. Note each code and its text, or take a screenshot. A code that returns in two days with the same description is far more informative than one you can no longer remember. It also helps to read the relevant live value at the same time, for instance the temperature or the throttle position next to a sensor code.
One reminder on numbers: Yamaha control units use two code generations, and sources do not always agree. The older FX140, FX1000, FX1100 and GP1300R differ from the VX1100 of 2005 onwards. When a forum number does not match the app, the app's description is what counts.
Clear after the repair, then test
The useful order is this: read the code, find and fix the cause, clear the memory, then take the ski out for a test ride and read it again. If the memory stays empty after a realistic ride, with the load and the running time under which the problem used to show, the fix probably held. If the same entry is back, the cause was something else, or only part of it.
Clearing in the middle of a repair has its place too. When you replace a sensor and want to see whether the old fault reappears, an empty list gives you a clean starting point. Just make sure you wrote the old list down.
When a code comes straight back
If the fault returns right after clearing, with the engine barely running, you are looking at a standing fault, such as a failed sensor, a broken wire or a plug that is not making contact. These are the easiest to chase, because the circuit is faulty right now and the live value will often show it.
A code that takes an hour of riding to return is a different animal. It points at heat, vibration or a connector that only opens up under certain conditions. For those, a recorded test ride is more use than another clear and a shrug. Logging a test ride describes how to capture that kind of fault.
A clearing sequence that needs no app
Some entries really are cleared with a simple action. On RiDE models, error 159 for the reverse gate is often caused by something banal, like a tie-down strap pulled across the stern eyes, a slightly bent rod, a loose plug on the RiDE harness, a relay or fuse, or the cable adjustment. After fixing the cause, the way to clear it is: engine off, pull the lanyard, wait 30 seconds, restart. If that does not stick, the cause is still there.
A word on what clearing cannot do. It does not repair anything, and it does not undo cavitation, a worn impeller, a blocked passage or any other mechanical cause, none of which the electronics log. If you look at a used ski, an empty fault memory only tells you it is empty today. It says nothing about what was in it last month.
The Yamaha edition of the M-JET Diagnostic can read and clear the fault memory on its 37 supported models, and more on the procedure is on the page about clearing the Yamaha fault memory.