i am able to replicate this. i am on the latest version 1.16.2. so if i am close to a pane or block of stained glass (any colour) about 1-3 blocks away the end crystals show but as soon as i am 4 or more blocks away the end crystals disappear and reappear as i move closer i have restarted my game(and launcher) and it still happens. on regular glass and panes it remains visible. before i started this i did check the known issues and was unable to find this one. also my game was unmodified or pure vanilla minecraft
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The issue appears to be locational (the distance required depends on the placement and direction of you and the end crystal), so this is how I was able to reproduce it.
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This issue is not present in the fabulous graphic setting and i forgot to check again in high graphics setting
Please provide a screenshot of your game with the F3 debug screen enabled.