Sutcliffe:
Is there a generally Problem with losing USB Connection after Upload ??
This last statement got me thinking... I've been assuming that the USB serial port is being created by the Yun, and then going away during execution. But based on what you're saying, perhaps you mean that after you upload a sketch over the USB serial port, when you go to open the Serial Monitor in the IDE, it says that port cannot be opened? If that's what you're saying, then it's a different situation.
Be aware that the USB serial port on the Yun has two different modes: application serial, and bootloader serial. They will actually show up as two different COM port numbers, and switch back and forth between them as you upload code.
For example, when I plug in my Yun into a serial port, I get the USB connected sound from my computer, and the serial port shows up as COM90. On the IDE Port menu, I select COM90. When I go to upload a sketch, the Yun gets reset and it enters bootloader mode: my computer plays the USB disconnected sound as the application port COM90 goes away, and then it plays the USB connected sound as the bootloader port appears, which in my case shows up as COM91. The sketch is uploaded, and then the Yun resets again to start running the sketch. I hear the USB disconnected sound as the bootloader COM91 goes away, and the USB connected sound as the application COM90 comes back.
This is all normal operation. But what I've noticed since upgrading my Arduino IDE a while back is that when the application port COM90 comes back, the IDE Port menu has the bootloader's COM91 port selected. The bootloader isn't running anymore (the application is now running) so there is no COM91. The application port COM90 is there, and ready for a connection, but the IDE has become confused and is no longer looking for it.
What I've found is that after uploading a sketch to the Yun, I need to go back into the IDE Port menu and re-select the proper USB port. After that, everything works properly until the next time I upload.
Could that be your actual problem? Perhaps the Yun is working just fine and it's the IDE that's getting confused?
Note that while this two COM port scenario is the same as other Arduino boards that use a '32U4 processor, like the Leonardo, it is different from the other Arduino boards that use a dedicated USB chip like the Uno. The Uno (and similar boards) only ever show up as a single USB port, so this kind of faulty port switching by the IDE cannot happen. While the processor may reset and go in and out of bootloader mode, the USB interface is independent on these boards, and the USB port does not change or go away during an upload operation.