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EDIT: I just noticed that I set the baud rate to 9600 for the instance and 115200 when initializing. After Deepsleep it may go back to 9600 again. I set it to 115200 and now I can receive data without reinitializing the uart.

(Old Solution)
I found a solution. I reinitialize uart.

if WakeUp == True:
            uart.deinit()
            uart = UART(1, 9600)  
            uart.init(baudrate=115200,tx=UART_TX,rx=UART_RX,timeout_char=10,timeout=10)
            print("Deinit UART")

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Answer selected by Dj-EKI
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