Ok so I have had the error 46 code twice now (5 years apart) and have used this forum and other sites to determine what the problem was , so thought i would collate everything into one post so others could fault find the issue easier.

So first things first is I would urge everyone to install a battery charge monitor light to make you aware of an issue BEFORE you get stranded at the side of the road with a dead battery.
something like this .

https://www.ebay.co.uk/itm/LED-MOTOR...-/200609174686


If you get the engine warning light and it results in error code 46 then it is a battery issue.
to fault find.
first things first. you require a Multimeter.
then test the battery , charge should be above 12v
and then test the charging system.

here�s how.

https://www.youtube.com/watch?v=1j9TXdIhInM

If the battery isn�t charging the first thing to check id the Reg/Rec plug. if its corroded or damaged then it may be issue. here�s how to change it.

https://www.youtube.com/watch?v=eHlpMSPzJQs

The connecter can be sourced by googling the part number RM14105R.

you can get them on eBay but cheaper here.

https://kojaycat.co.uk/epages/950000...oducts/KYG6WAY

Next step is to test the reg/rec itself to determine if its Gubbed or not.

Heres how.
https://youtu.be/-2jWIkhy1fo

and also how to test the stator whilst you�re at it.

https://youtu.be/NSV8iU65bH8

and here�s a link to the workshop manual. page 8-56 for stator values.

http://www.xt660-club.hu/Media/Yamah...ere_Manual.pdf

Also last word on this issue is resealing the badly designed plug.
I haven�t been able to determine for certain that silicone is non conductive to reseal the plug to avoid water ingress. A friend who builds modular synths tells me that Hot glue from a glue gun is non conductive, if you don�t have one then i would also recommend .

https://www.screwfix.com/p/self-amal...SABEgLRGPD_BwE