Transverter jack on Flex6300

Using the XVTR BNC jack as a RX only input begins with the ANT selection window, by selecting the XVTR jack as the RX antenna, but not the TX antenna. This will prevent transmitting low level RF output into your outboard 6 meter preamp.

I don't think the second part of your question has been addressed, i.e., whether the output level of your external 6 meter preamp could damage the front end of your Flex receiver.

While I don't use an outboard receive preamp on 6 meters, I regularly use the XVTR jack as a receiver input for a DX Engineering magnetic loop receive antenna on the lower bands. The mag loop has a high-gain preamp at the antenna end of the coax, which is always on. The preamp has not caused any problems with the front end of my Flex receiver. So, depending on the output level of your external 6 meter preamp, you should be okay. You might want to compare the specified output voltage of your preamp with the spec's. Flex can provide on the maximum safe input voltage on the Flex receiver front end if in doubt. While Flex does not provide schematics, I assume there is diode protection on the XVTR BNC input. Staying under the diode protection voltage level would avoid a trip back to Austin for your rig.

I agree with an earlier comment in this chain that you may not need the outboard preamp, since the Flex has a pretty nice built-in 6 meter preamplifier. You might find that cascading preamps does little to improve the signal to noise ratio of the received signal.