Training that has too much low force pedaling (quadrants III and IV) likely recruits fewer muscle fibers which may then result in loss of oxidative capacity in those fibers. In addition, there is almost certainly a decline in neuromuscular power. Either, or a combination of both, is responsible for "ergometer syndrome." Neuromuscular adaptations occur rapidly but retraining oxidative capacity may take awhile. Capillary density is probably not affected since it is an extracellular adaptation. Mitochondrial density, however, may be subject to the "use it or lose it" principle and fibers not recruited will "lose it." Thus, I hope erg' syndrome is more of the former and less of the latter.
The solution is fairly straightforward. Indoor riding and especially ergometer riding is generally very time efficient and allows for very focused training. With the increased training efficiency, one has the extra time to add L5 and perhaps even L6 workouts to provide the needed high force pedaling. L6 efforts are likely too short for any meaningful aerobic adaptations so if erg' syndrome is due to lost oxidative capacity in a population of muscle fibers recruited primarily during high force pedaling, L5 workouts or even efforts in the upper range of L4 would be more effective.
One idea was to insert occasional power spikes into SST ergometer rides. Like L6 training, that likely would not help oxidative capacity. Another problem was that it increased the perceived exertion of long SST rides, making them far less tolerable.

Four plots on the same chart.

QA plots of ergometer rides can be weird. This one looks almost like some sort of crop circle. Note how small the cloud is and how it's all relatively low force pedaling. This is representative of most of my training for the past few months.

Road race with some fairly big hills.

My first L6 workout in a long, long time. The uppermost cloud is the L6 workout on a short hill. The cloud below it is the tempo riding I did afterwards. Pedaling force is quite a bit more than on the erg.

Training ride with several long climbs. Some steep sections where I ran out of gears.

3x20 at 295W on the erg. Rest intervals were 5 min at 145W. Notice how the data points follow the 295W and 145W power curves so closely.

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