What we do know:
Before the Sovereign Grant came into being, the costs of maintaining royal residences came from the Grant-in-Aid for the Maintenance of the Royal Palaces paid by the Department for Culture, Media and Sport. There were never enough funds available and although the Civil List had a surplus, that surplus couldn't legally be used for maintaining the palaces. Consequently, a number of buildings were maintained or repaired in a timely fashion, meaning that when work was done of them, it cost way more than it would if it had been done sooner.
When the Civil List was abolished and replaced by the Sovereign Grant, the three Grant-in-Aid were also done away with. All the money for running the monarchy went into one big pot. Spent less on travel in 2015? Great, that meant there were more funds available to be used elsewhere.
A list was drawn up to prioritize which buildings would be worked on when. According to Wikipedia:
In the early 21st century, Frogmore Cottage was a series of five separate units housing Windsor estate workers.[12] In 2019, it was provided to the Duke and Duchess of Sussex as a grace and favour home by Elizabeth II,[13] and converted into a four-bedroom-and-nursery single-family home at a reported cost of £2.4 million from the Sovereign Grant prior to the birth of their son, Archie, in May 2019.[14][15] As a property of a royal palace of state and designated heritage site, Frogmore Cottage was scheduled to be renovated in any event, regardless of occupant.
It's interesting that the Harry's use of Frogmore Cottage was deemed grave-and-favor (presumably switched to "sign a lease, sonny boy" when he ceased to be a working-royal). Anyhow, if the costs of repairs, upgrades, and maintenance of Frogmore Cottage on the Windsor Estate was deemed to be the responsibility of the Sovereign Grant, why would Royal Lodge or any of the other properties on the Estate be treated differently?
Info about Frogmore Cottage
Info about Sovereign Grant
Info from 2005 given to Parliament regarding four "royal" leases
111