Ok, found the solution to this problem. I am sure most gamer already knew how to fix this but I am still writing this in case someone has the same problem as mine.
(1) make a backup of the map (the whole folder) in case you screw up.
(2) open your map then click tab "Marker" then click "Layer", Then
turn off all the buttons for "Basic" layer but
turn on all buttons for "Path" and "AI"
(3) Turn off the Symmetry (to none)
(4) window select all markers on the map
(5) Click tab "Marker" and at the bottom menu, click Export
(6) once exported all markers then press keyboard button "delete" (to delete all markers that have sunken on sea bed)
(7) save map then reopen the same map then make sure the you have turn on the water (in tab Terrain/water)
(8) Click tab "Marker" and at the bottom menu, click Import ...
your markers should now stay floating on the water (took me awhile to figure this out
)