The glycogen was refilled and the enzyme that spends it was still turned down

What pyruvate dehydrogenase is

Pyruvate dehydrogenase is the enzyme complex carbohydrate must pass through to be burned aerobically, and it cannot be bypassed. Measuring its activity separates two things a breath measurement cannot, which are having carbohydrate in the muscle and being able to push it through the gate quickly.

Drawn from background physiology, not from this paper.

Why they ran it

It was already established that five days of a high fat diet while training, followed by one day of carbohydrate restoration, raises fat oxidation and lowers carbohydrate oxidation during cycling. The authors state that the mechanisms responsible were unknown, and expected them to involve the regulatory enzymes on both pathways moving in opposite directions.

Drawn from the paper's introduction.

Seven male cyclists completed the same protocol twice in random order. Five days of either a high carbohydrate diet at 10.3 grams of carbohydrate per kilogram per day, about 70 percent of energy, or an isoenergetic high fat diet at 4.6 grams of fat per kilogram per day, 67 percent of energy, both alongside supervised endurance training. On day 6 everyone ate high carbohydrate and rested. Day 7 was the trial.

The carbohydrate restoration worked. Resting muscle glycogen was 873 micromoles of glucosyl units per gram of dry weight after the fat week and 868 after the carbohydrate week. Those are the same number.

The fuel mix was not the same. During cycling at 70 percent of peak oxygen uptake the respiratory exchange ratio was lower after the fat week, amounting to roughly a 45 percent increase in fat oxidation and roughly a 30 percent decrease in carbohydrate oxidation.

Pyruvate dehydrogenase activity was lower after the fat week at rest, throughout the cycling, and during a one minute sprint. During the cycling it was 1.69 millimoles per kilogram of wet weight per minute against 2.39. Estimated glycogen breakdown was also lower after the fat week, 9.1 against 13.4 glucosyl units per kilogram of dry weight per minute in the first minute of cycling, and 37.3 against 50.5 during the sprint.

Hormone sensitive lipase activity was about 20 percent higher after the fat week during cycling, but at P equals 0.12 that difference was not statistically significant and the paper reports it as such.

The numbers

Resting muscle glycogen, fat adapted arm	873 plus or minus 121 micromol glucosyl units/g dry weight
Resting muscle glycogen, high carbohydrate arm	868 plus or minus 120 micromol glucosyl units/g dry weight
Change in fat oxidation at 70 percent peak oxygen uptake	about 45 percent higher after the fat week
Change in carbohydrate oxidation at 70 percent peak oxygen uptake	about 30 percent lower after the fat week
Pyruvate dehydrogenase activity during cycling, fat adapted	1.69 plus or minus 0.25 mmol/kg wet weight/min
Pyruvate dehydrogenase activity during cycling, high carbohydrate	2.39 plus or minus 0.19 mmol/kg wet weight/min
Glycogen breakdown, first minute of cycling	9.1 plus or minus 1.1 versus 13.4 plus or minus 2.1 glucosyl units/kg dry weight/min
Glycogen breakdown, one minute sprint	37.3 plus or minus 5.1 versus 50.5 plus or minus 2.7 glucosyl units/kg dry weight/min
Hormone sensitive lipase activity during cycling	about 20 percent higher after the fat week, P equals 0.12, not significant

Why this might happen

Shown in this study The study measured this step directly.

The authors conclude that the previously reported fall in whole body carbohydrate oxidation after fat adaptation is a function of metabolic changes inside skeletal muscle. Pyruvate dehydrogenase, the gate carbohydrate must pass through, was turned down and stayed down through exercise, and glycogen was broken down more slowly, so the capacity to use carbohydrate was reduced even though the supply had been fully restored.

They are explicit that the upstream signal is not settled, saying the metabolic signals responsible during the moderate cycling remain unclear.

Drawn from the paper's stated results and conclusions.

What this does not show

It does not identify what turned the enzyme down. The authors say directly that the metabolic signals responsible for the shift during cycling at 70 percent remain unclear. They offer lower accumulation of free ADP and AMP as a possible cause for the sprint findings, and they do not claim to have shown it.
It does not show that the athletes were slower. There is no performance trial here. Twenty minutes of cycling and a one minute sprint are measurement protocols. What a lower rate of glycogen breakdown does to a race is a separate question this study does not ask.
The lipase result is a non finding, not a finding. The roughly 20 percent higher hormone sensitive lipase activity carries a P value of 0.12. It should be read as no detected difference, not as a smaller difference.
Seven male cyclists, one day of restoration. A small crossover in trained men, with carbohydrate restored for a single day. Whether two days or five would have closed the enzyme gap is not tested here.

Where this leaves us

Refilling the tank and being able to use the tank are now demonstrably different things. Five days of fat adaptation left muscle glycogen fully restored after one carbohydrate day and still left the enzyme that spends it turned down. This is the study that gave the reciprocal switch a measured location rather than a respiratory inference.

Seven trained male cyclists, five days of diet with training, one day of carbohydrate restoration, twenty minutes of moderate cycling and a one minute sprint.

A design that varies the length of carbohydrate restoration and tracks pyruvate dehydrogenase activity across it, which would show how long the suppression actually lasts.

Caveats worth holding

Muscle glycogen here is expressed per gram of dry weight, which is roughly four times the wet tissue figures used in some older loading studies. The units are not interchangeable.
Seven cyclists in a crossover, with repeated biopsies from the same muscle across two trials.
The hormone sensitive lipase difference did not reach significance and should not be reported as an increase.
One day of carbohydrate restoration was tested. Longer restoration was not.
The full discussion was not openly reachable, so the mechanism section rests on the paper's own stated conclusions and its explicit statement of what remains unclear.
Male cyclists only.