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The girl I was talking to in the back looked like she was on the verge of tears when she realised what happened so I didn't push it. They told me there was no way they could make it clear any faster, all the could do was cancel it and for me to ask the customer to pay again by bank transfer. As it was only two days I decided not to hassle my customer and just got them to pay it in straight away.
Funny thing is they always try and get you to use the little letter box things for paying in cheques but I've always been sceptical about them, I'd rather wait in a queue and get the cashiers stamp. I'll definitely stick with that now, might have been a lot harder to solve if I didn't have proof I paid it in.