Checked off on the map? Right click and the icon disappears...left click will place a red X on it.
Same with most icons...exception being your grave marker if you die...it stays until you die again.

You can fight any of the bosses multiple times forever and ever. The location stones are relational to that area’s boss. Each boss potentially can have multiple summoning locations on your seed/world.

For the powers you only hang the trophy once but you can collect extra trophies for decorations. And you can choose to fight the bosses multiple times for XP/fun.

https://valheim.fandom.com/wiki/Progression_guide

You hang the trophy and the only place its gets "checked off" is visually at the spawn shrine, and the notebook that resides inside your own mind.

Don't mind the bosses not being 'checked off' in the map. It doesn't seem to do anything. Not sure why some aren't checked off, but since I play co-op, it may have to do with that it's not me dealing the final blow or something. Still doesn't matter. You can move on and search for the next boss/marker at your leisure.

Originally posted by Questionable:

I killed the elder, put the trophy on the hook... still he won't get checked off.

When I find locator pts, they keep locating Elder still.

I summoned him again and killed him again. Can't hang the trophy again cause its already done.

Am I missing something?

Are the locators that you are using in the Swamp? If not they won't help you find the 3rd boss.

Also you don't have to hang the trophies to go on to the next boss. That is just to unlock the abilities.

"checked off" ? of what?

locators work based on location meaning in bf you will always get elder locs, and in swamps always bonemass etc.