A bypass harness is a wiring harness used to bypass the original truck OEM wiring to the engine ECM. The harness has everything that the engine needs to run. It has a data link connector used to communicate with the ECM. In addition, there is a throttle connector so that you can plug in a throttle and rev up the engine. The large alligator clips make connecting to a power supply fast and easy.
A customer stops by in a hurry and wants you to plug in to see why the check engine lamp is on. However, your service tool cannot communicate because the truck has a damaged wire at the diagnostic connector or ECM.
If you have a bypass harness, you could plug in directly into the engine bypassing the broken wire. Allowing you to read the faults and advise your customer.
You have just finished swapping engines in a truck only to find that the "good engine" you just put in has problems.
If you have a bypass harness, you could have tested the engine first, ensuring that the engine was free from defects (e.g. leaking, missing, smoking, vibrating, faults).
Engine cranks but won't start.