I have a Crimson II kit I purchased used about 9 months ago. Everything has been working great but today the floor tom is only sensing the rimshot. I've plugged the floor tom cable into a rack tom and the problem remains. I used a new TRS cable to connect the floor tom pad into the Tom 4 input on the module and that works so the pad is not at fault. All this indicates to me that the floor tom cable in the harness is bad. Do I have to replace the entire harness or can I just replace the bad cable in the harness? Any advice on attempting to repair or replace the cable in the harness connection?
If you purchased New it should be under Warranty..
Unfortunately that's the major issue with DB25 Harnesses and it's hard to diagnose without having a 2nd harness or another module.
The issue could be with the molded 1/4" end..the cable end to the connector/pins..or the Internal Module/connector(female) which is soldered to the Main board and also has a resistor for each Trigger/ solder point ...so there are a lot in the chain that can go wrong.

If you had a 2nd harness and the issue remained it would be at the Module connection or a resistor..if there is no issue with the 2nd harness then the probability is the Harness.
The connection (male/pins) from the harness into the module is molded so there is not much you can do there other than using a Multi-Meter and checking continuity between the 1/4 male end and the pin assignments and if the cable end is bad solder another TRS Male on.
The cable could also have pulled away from the Pins.I have seen many of the Harnesses including some I have that the insulator has pulled away from the 25 Pin connector Molded Housing,exposing the wires..typically Black/Red/White and become a very weak point.
Trying to pry it open will only make matters worse and probably ruin other connections.
Medeli DD650 (Command,Crimson,II,DM10 Studio MKII,Forge) all use the same DB25 Harness..the difference between them is/was Firmware/Hardware and Triggers.

You could try and unplug/plug a few times and see if that helps with the contact (if that is the issue)
Also to double check and make sure...I posted years ago how you can place the Medeli DD650 Modules into Test Mode..and test the trigger if the harness is good , however it doesn't help much if you are sure the trigger is working properly and aren't sure if the issue is the Module connection or the DB25 Harness.
That's the Major problem with DB235 harnesses..if you stretch a cable to far..or pull too hard they are easily damaged.
If you connect to the module and are a little off and force it.. you bend/break pins..if it's a resistor that went bad you won't know without tearing the Module down and equipment for checking.
Medeli DD650 (Command,Crimson,II,DM10 MKII Studio ,Forge) Module Test Mode ...Press and Hold Down+Up buttons simultaneously while powering on ..you'll see the Alesis splash screen..Firmware Version .. "Booting"..
Then you'll see the main menu ...use the up/down buttons to maneuver...press down to pad test which is #2...press enter
There will be a PAD... and Value...
The "Pad" will show which trigger is being hit or in this case pressed..the "Value" will show if the hit is detected and what velocity...a hard hit should show around 127..it should vary with a variety of velocity hits.
To "Exit"..go to 8 erp..the module will power down.
Here is a Link for
Warranty RepairInMusic also started adding third party Repair Centers for "After Warranty"..however I only see 2 currently in the USA and Numerous in Europe.
The bottom line is ..it could be as simple fix (New harness) if you are aware of any damage that occurred to the harness ..otherwise process by elimination or send the module/harness in for repair/service
EDIT:Added Links..Images