The high-water mark is the highest value the fund has reached. It only ever goes up. A fund only burns its coin when it is above that mark, so a fund that loses and then wins back the same amount has not made a profit and burns nothing.
Fees that arrive between trades sit in the fund wallet as SOL. They count toward the fund's value straight away, and they are part of what the agent may trade, inside the limits.
Bips is not live yet. This page describes the design and may change before launch.