I found in my servers that if I turn on /fly and go to any height I can double tap my spacebar and fall hundreds of blocks without dieing. I can also jump off a bunch of blocks high and not take any damage. This only occurs if I've turned /fly on.

I've tested EssentialsX with 1.13.1 and the 1.13.2 (Build 403) of PaperSpigot and they both have the same behavior. I don't recall reading anything that if a player is given fly permissions that they won't take any damage if they fall. So I went from 70 plugins down to just the ones I needed on a vanilla server (LuckPerms-Bukkit-4.3.2, EssentialsX-2.15.0.52 & Vault 1.7.1. I was able to reproduce.
Plugins

Full startup log: https://hastebin.com/aqisikayon.md

Has something changed or is this a bug? I am an admin and OP level 4, but that has never been an issue in prior versions that I remember.

I get the feeling that this may be a change made to the server software somewhere along the chain. EssentialsX does not actively block fall damage when flight is enabled, so this needs some further investigation.

Edit: I don't think you ever took fall damage when flight was enabled, so I'm not sure anything changed?

I don't think it's a bug. This is how Essentials has worked for as long as I can remember.

I've been enabling fly mode since pre 1.8 days to avoid fall damage while jumping aimlessly around the world

I spun up both a 1.8 paper and spigot server and tested with the latest Essentials on Spigot. Fall damage is blocked when you're in fly mode.

Thanks to @pop4959, @electronicboy and @Tofuus for confirming my suspicion.

@smmmadden As there doesn't seem to be any indication that this changed, could you try and replicate this on a non-1.13.x server?

I just set up a 1.12.2 server and retested and you are all right. No damage taken if /fly is enabled no matter whether you are flying of fall off the face of a cliff and not flying. Very odd since I've been playing since 1.9 days and never noticed it. I just made sure I didn't fall all these years. lol

I always thought that if I had fall damage enabled that it didn't matter how I fell. Is there any way that if I did turn on /fly that it look at this setting to determine if fall damage should be maintained?

Thanks!

This is vanilla behaviour and is not at all related to EssentialsX. /fly instructs the server to turn on fly mode for a specific player, and a side effect of that is that fall damage is disabled by the vanilla server.

protect.disable.fall is part of EssentialsX Protect and is not at all related to EssentialsX's /fly.