You must be on a different version of eBay than me.

If a buyer opts for local pickup, I have the option to mark 'picked up'. Done it many times.

"If a buyer opts for local pickup"

In pick up ONLY items ( which the OP's was)  I've only ever had the option to enter the QR code, no option  to mark as picked up at all.

I don't use the app.

I don't use the app.

Neither do I.

I can only relate my own experiences, which I have.

And I don't do pickup only. There are far more productive avenues to sell stuff locally.

"And I don't do pickup only"

That's probably the difference then. 

If it's pick up ONLY  (which the OP's was)  the code has to be entered.

It's obviously nothing to do with the app,  as in this thread Bricks wrote:

Confirm Pick Up

Enter the buyer's 6 - digit code, located  in their confirmation  email

"This is the only option I have available to mark as picked up.  App is the same"

https://community.ebay.com.au/t5/Selling/Buyer-paid-cash-on-pickup-and-didn-t-receive-a-code/m-p/259...

That's my experience too.

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@*casey* wrote:

 

If it's pick up ONLY  (which the OP's was)  the code has to be entered.

 

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That's not entirely true, if the purchase isn't made through eBay - ie by cash or through the sellers bank account etc - then the MBG isn't applicable and the code is not needed.

Yes, that's what I already wrote

"The QR code is only needed in case the buyer claims an item not received and has paid  with an eBay MBG  payment option"

The OP asked how to mark as picked up ...............and I told the OP to forget it.

Yes, I only accept cash on pick-up…..so I just mark as ‘paid’ and ‘sent’…no code needed