Like HW said, the 6900's were worn out after a long service life.
Why weren't they rebuilt again? Various reasons:
They were a non-standard model with many unique parts. The engines were 645-E3A tweaked for higher horsepower than a 645-E3 as used in hundreds of SD40-2's. Injectors, camshafts, turbocharger etc were different parts from SD40-2's. They were predecessors for development of the GP40X and 50-series locomotives. They were the first production locos to have plug-in modular electronics, which became standard on the dash-2 series.
They were all geared for higher speeds and generally used on hotshot trains, often MU'ed with "8000" series SD40-2's which also had the high-speed 59-18 gear ratios. The 6900's were not used on run-through trains to other railroads AFAIK. They served a somewhat specialized niche.
The unique 8-wheel trucks tended to wear flanges on the #1-4-5-8 axles of each unit because of the longer truck wheelbase. Not an optimum arrangement for modern diesel power.
About 1980 the FRA came up with a new rule requiring that locomotives used for any road switching must have bottom steps with 9" horizontal clearance, so a crew person could stand without needing to use both hands to hang on. Locomotives which didn't meet that rule could only be used in the trailing positions of an MU consist. There was no practical way to modify the 6900's to comply.
In 1980 the FRA had new noise abatement rules for locomotives. EMD installed exhaust mufflers and developed quieter radiator fans for new locomotives beginning in 1980. That's why older high-HP locos may seem louder under load.
North Platte 1980