I was on a huge mining trip on a server with keepinventoy on, and I stored all my loot in my deep pockets 3 leggings. Once I was done, I wanted to reset by removing all my armor, including my leggings, that went into the extra inventory space via shift-click (since my actual inventory was full). And just like that, I lost everything. My armor, my three stacks of diamonds, my 15 netherite ingots. I gambled all my xp away, getting a different pair of leggings with deep pockets 3, just to find out that the inventory got cleared. I want everything back. Please.

Just tested it: with no other mods, taking off your Deep Pockets leggings (e.g. by moving them into the Deep Pockets section) causes all items stored in Deep Pockets (now including the legging) to drop in front of you like if you've tossed them away manually.
Do you by any chance have a mod installed that clears out dropped items?

I do not believe I do. All the items just disappeared.

I'll take note. Can't think of an exact reason why that could happen. My guess - mod conflict.

Our server has diggus maximus and inventorio, nothing else. I use around 90 client-side mods though, but I don't think they can interfere with inventorio, right?

Doubt so. Can you send the logs from the time when the items got lost if you know the estimate time when it happened? Logs located at .minecraft\logs

Sadly, I can't access the logs since I'm not a mod... I asked the owner but they are currently offline. Is there any other way?

Don't think so. The only lead right now is any potential errors in the logs related to Inventorio.