Issues with payslip - first time buyer

Hello! I am a first time buyer looking to get a mortgage. A few months ago, my workplace overpaid me. I told them before they paid me that they were going to overpay me but they did it anyway (work for the NHS, classic). Now they want to take the money out of next months payslip. Money wise that’s fine for me, I can afford it as currently living with my parents whilst saving for deposit. However I’m worried that as I’m planning on applying for a mortgage soon that this might affect how much I can borrow and lenders might not be very happy that one month I have been paid about £1000? Soon I am also due to change jobs and will have a significant pay rise which will be my future salary ongoing. Am I best to repay this money to my workplace another way or is it ok for this to be taken from my payslip? Appreciate peoples advice and knowledge, thanks!