Lake height is calculated for every basin, and there is a lake if lake height is higher than ground height. If it is lower, there is no lake.
In that case, it was previously raised to ground level, but since this can be done in Lua, we can write initial lakes height in the files.
This has the advantage of reducing file size, since there are bigger areas of equal values, that are more efficiently compressed.
Gael-de-Sailly