When you enter a boss room in TP, there is always a cs before the fight starts (either immediately after entering or tied to a trigger). If you skip a cs in TP it often reloads the area with a fadeout to avoid bad looking transitions. But since the area gets reloaded, the cs would play again in an endless loop. To avoid this the programmers used flags and upon skipping the cs the flag gets set to a high number and quickly counts down to 0. If the area gets loaded again and the flag is not 0 the fight will be started immediately. Same happens if you void. If you reset during such a void in a boss fight the flag can't count down to 0 and remains at a high number. The flag is not changed to 0 upon soft resetting either, only a hard reset clears it.
Reset during voiding in the King Bublin 1 fight gives the flag at a high number because the King Bulbin 1 fight uses the flag
Skipping the sacred grove 1 (EMS) or second grove 2 (before tot) cs sets the flag to 1 without changing it back to 0 due a programming error in the way the sacred grove is handled (if you void or die in the grove the area state gets set back to the beginning and you have to howl again).
/!\ Be careful, if you void right before Monkeys in Forest Temple or if you do a hard reset before having finish the Deku Toad Fight instead of a soft reset(X + Start + B) it cancel the glitch /!\
Having the flag at 1 or higher results in a lot of early bossfights (KB 1 or sacred grove cs can be used so far). However most of these early bossfights are not useful due to the time it takes to set-up.
To save memory the game uses the boss flag to check how many monkeys you saved. Using the grove cs sets the flag to 1 which doesnt change anything noteworthy, as you need 4 monkeys to progress normally. Using KB 1 void reset however sets the flag to a very high number. Since this number is higher than 4 usually, the game will give you 4 monkeys from the start (maximum). This allows you to swing over to Ook the first time you visit the outside area.
A faster method to set the flag high enough is the skip the CS of KB as you soft-reset (X-B-Start). This saves having to ride to the edge of the field and jump off. It is important that you start the soft-reset first when you see the CS starting and then mash start to CS, doing it the other way round will not work