Hi I have an issue with customer deposit and customer payment in USD currency and the invoice in different currency How can I apply it to the invoice in different currency

Just apply payment to the invoice. You already have everything else. Revaluation will take care the FX issues

Hi Need to mention that the base currency is in a different currency Payment in USD Invoice in EUR Base currency in EGP

You can not apply those two transactions. You either have to change the invoice or the payment transaction.

We have a painful work around, that isn't ideal for when you can't get the customer to pay in the sub base currency or bank account currency. We journal the payment in and receive into suspense account (GL code) in the payment currency, then journal out of suspense onto the customer (debtors/receivables GL) in the invoice currency. The first journal will work on your bank rec, the second will show on your payment allocation screen for the customer. There will need to be third journal to deal with the FX balance on the suspense account. Painful, but it'll get the job done.

@Ahmed Hamdy - just apply the payment, it will be in, say, EUR, and your actual cash you already have (!) is, say, USD. The variance between EUR and USD will go on P&L into FX related gains/losses

@Karina No, you can not simply apply a payment in EUR to an invoice where currency != EUR.

There is no way to that