It was probably the clean out that did it. He was maybe a bit confused as to where his toilet corner was if everything smelled clean, so scent marked three
It isn't really necessary to clean them out every week and it does tend to make them pee on everything to scent mark it if all their scent is completely removed.
If you have deeper substrate, you can just spot clean the whiffy areas and only need to do a big clean out every 6 to 8 weeks or even longer. Also it gives them more to dig and burrow in. You just take out a handful of the whiffy substrate and replace it with a handful of new and mix it in so it still smells familiar. A litter tray really helps as well. I used to use a corner a litter tray with chinchilla bathing sand in - if you put a little bit of their pee'd in substrate on top, they tend to use it. Then you empty the litter tray and clean it out every 5 days or so (it might go 7 days) and replace the sand - the rest of the cage should stay clean mainly - unless your hamster pees on everything!
Also when doing clean outs its a good idea not to clean everything at the same time. So if you change the substrate, then do the wheel a different week and the toys a different week again, that way something always smells familiar and they don't panic and pee on everything in sight.
Even when I change the substrate, I don't change all of it - I remove the top half, keep the bottom half (if it's deep enough the bottom half is usually dry - or keep the dry half anyway), wipe the cage base with a warm damp cloth and dry it, replace the clean half, add new substrate, and mix it in - so it still smells a bit familiar and they accept the clean out better
As for which corner to put a litter tray in now - I would just put it in one of the corners he is using. He should start using it if he's using three corners and will probably come back to it as the main one. If not, then wait a bit to see if he settles on one corner then move it there
Our last hammy used to let me know if it was getting whiffy and needed changing and would neatly put substrate on top of the sand lol.
This one works quite well
https://www.amazon.co.uk/d/Houses-Ha...Hamstery+potty
Not sure how much substrate you have now, but if you fill the cage base to within 1cm from the top and have it a little bit deeper in the centre, they tend to like digging in it and moving it around and building mountains. It might use up a lot of substrate initially, but overall you use less as you can spot clean most of the time and do clean outs less often.
This is the Chinchilla bathing sand. It's safer than potty litter and soaks up the pee well. One of those lasts me a good few weeks.
https://www.amazon.co.uk/Supreme-Pet...hinchilla+sand