This bug happens randomly, making everything turn transparent except for generated structures and blocks placed by players.
This glitch can be 'fixed' by updating my Graphic Driver, but a similar glitch occurs, with noticeably less frequency.
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Is this still an issue in the most recent versions (currently that is 1.13.2, or the latest snapshot 18w46a) of Minecraft? If so, please update the affected versions and help us keeping this ticket updated from time to time. If you are the owner/reporter of this ticket, you can modify the affected version(s) yourself.
Happens very often (for me), especially in SMP / Multiplayer / Survival Servers. (Affects Singleplayer world / integrated server too, but more rarely and in certain situations only).
When flying with Elytra (for example) there are a lot of Flickering / Glitching Chunks / Terrain around the Player and this causes very often to collide against invisible mountains or trees. Also re-loading the world (or restarting the server) does not 'fix' this issue.
The only 'fix' is Reloading the Chunks (F3 + A) or interacting with manually placed blocks in the invisible / not-rendered terrain / area.