Usually higher levels of liver glycogen are related to higher levels of bodyfat. Most of the time when one has full liver glycogen, blood glucose levels are high and the body is anabolic which means that externally digested glucose, AAs and FFAs are stored as glycogen, protein and triglycerides (fat).
When liver glycogen becomes depleted, via intensive exercise or the absence of dietary
carbohydrates, the liver shifts roles and becomes catabolic. Glycogen is broken into glucose, proteins are broken down into amino acids, and triglycerides are broken down to free fatty acids.
The majority of T3 is not released from the thyroid gland but rather is converted from T4 in other tissues, primarily the liver. Thus, when you are in the second glycogen depleted state, the liver is not able to fully convert the T4 to T3.
Mr.X