Whenever there is lightning in front of water, stained glass, entities, and tile entities they become invisible from that point of view. Occurs when graphics are on fast or fancy.
I found the problem for
skeleton skull
dark oak sign
nether portal
water
clouds
ice
end portal
ignited tnt
zombie
chest
the bug didnt occur with:
lava
normal glass block and pane
relates to MC-44244
Linked issues
clones 1
is duplicated by 14
MC-188511
you can't see the water through the rays
Resolved
MC-191685
Lighting strikes "delete" water for split seconds - Texture issue
Resolved
MC-196598
Nether Portal is invisible if seen through lightning
Resolved
MC-198846
Lightning Bolt making water Invisible
Resolved
MC-206236
when you summon lighting in water you can't see the water when the lightning overlays it
Resolved
9 more links
Just switch to Fabulous graphics