Flags is a property that is only used with a few different elements. It is not saved. There are currently 4 different things stored in flags:

0x1: "Stagnant" - Used by energy particles and water when a particle can't move, to reduce lag by not performing as many checks next frame.
0x2: Skip movement for one frame, only works on PHOT (used when created by powered clones)
0x4: used for water equalization, to keep track of which particles have been checked
0x8: Compatibility flag, which allows sponge to move, or photons to be decorated. (for compatibility with older saves)