diag: Enable hdlc encoding in case the logging mode changes

Currently hdlc encoding is not turned on by default in case if
the logging mode is changed from usb mode to memory device mode
or vice-versa. By design, the hdlc encoding must be turned on
after any logging switch. Also, stop any further reads over
peripherals until the time the mux layer is established.

Change-Id: I21f89771412e2da8ee0243f5f6bb24f917038300
Signed-off-by: Katish Paran <kparan@codeaurora.org>