How can I resolve a situation in which my Mac keeps crashing while working with a specific video file?
No-one here is going to be able to give you a 100% definitive answer on why a specific video file is causing a crash (especially without full details of the file in question and without access to it), except of course to say it's most likely corrupted in some way.

Some things to try include:


Booting your MBP into Safe Mode and trying to import the file again.
I know you've tried re-encoding the file using Adobe Media Encoder, but perhaps you could try encoding the file into a totally different format first. Ideally you would try doing this within the Atomos Shogun Flame directly, but I'm not familiar with that device and don't know what export/editing functions it has. If none, have you got any other software to try converting it?
Another thing to try would be to manually copy the file from the SD card onto another card/drive (or to your Mac) without going through an import process. If that succeeds, then try importing the file (or converting it into a new format) from the new location. 
Open the file using Quicktime Player and, assuming it opens okay, use Quicktime's export function to export it (with a new filename). Then see if the newly exported file can be imported into FCP and edited fine.
Take a look at your FCP preferences to see if changing how it deals with situations like dropped frames will make a difference.