Dennis, keep your comments directed at helping the OP, and stop worrying
about what I'm saying.  We're obviously not talking about the same thing,
and your comments to me are not helping the OP solve his problem.

David,

As an example if I run the following program there is no data loss:
>
> import serial.tools.list_ports
>
> # connect to the BBB serial port on Windows
> x = serial.Serial('COM9')
> x.write(b'yes "123456"\n')
>
> while True:
>        received = x.readline()
>        if received != b'123456\r\n':
>                 print(received)
>
> But there is data loss if I run this:
>
>     import serial.tools.list_ports
>
>     # connect to the BBB serial port on Windows
>     x = serial.Serial('COM9')
>
>     x.write(b'yes "1234567"\n')
>
>     while True:
>         received = x.readline()
>         if received != b'1234567\r\n':
>             print(received)
>

This seems to me that you are indeed overflowing your buffer. How or why
I'm not sure, but if sending 6 characters all is fine, and 7 characters
does not transmit properly then obviously something is wrong. I'd look into
googling the driver name this device uses against any known reliability
issues in Linux. One odd thing I did notice about your output you've shown
us, is that everything in your received = x.readline() loop seems to be
working fine.But all the failures are related to this, or a similar line
you've not shown us yet: x.write(b'yes "1234567"\n')

I'm suspecting you're not showing us all your code however. Because the
output you've shown us does not necessarily "jibe" with the code I'm seeing
here.

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