On my iPad, the sum of my world's data sizes in the Minecraft app is 5.4 GB (2.6 GB, 2.5 GB, and 300 MB). The Minecraft app container's data has an iCloud Backup footprint of 32 GB as reported in the Settings app. I would expect the iCloud backup size to be similar to the total of the world sizes; a 6x multiple makes it seem like the app must have orphaned some files inside the container. I don't want to lose my worlds, yet this is causing me to run out of iCloud storage so I'm not able to run an iCloud backup at all (unless I exclude Minecraft from backups).
My preferred solution is obviously for Minecraft not to do this in the first place, but as a backup measure to scan for and remove stray files during initialization; essentially the on-disk moral equivalent of garbage collection.
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I'm quite sure MCPE-161293 is not the same issue. Yes, aside from calling it "iPad Storage" instead of "iPhone Storage", it has the equivalent menu. When I go there, I do see a good dozen or more "mystery meat" files, but they are only up to hundreds of KB in size, so they are noise in the equation.
However, exploring this a bit further, I am thinking this might be more of an iPad OS and/or iCloud issue than a Minecraft issue. In the name of science, I tried one more manual iCloud backup and after it thought for a minute I saw the familiar prompt that the backup was too large for the available iCloud space. Next, I turned off Minecraft backups in the iCloud Backup settings. That has the side effect of deleting the old cloud backup for this app container. Before I toggled it, it was still showing a 32 GB backup size for the Minecraft container. I completed a manual backup successfully without Minecraft, then turned Minecraft's toggle back on. After that, to my surprise, I ran yet another backup to completion including Minecraft, and the iPad Settings app showed its backup size as... drumroll please... 5.4 GB, very well aligned with the sum of the world sizes.
Given these new findings, my estimation now is that iPad OS is in error when calculating whether it can complete a backup. It might be falling prey to the familiar problem in any backup or synchronization endeavor where the total size might be fine but due to the order of traversal, it first finds a bunch of stuff to add to the backup before getting to stale items it can remove and pessimistically quits too soon with the false claim that there isn't enough space available. Furthermore, the size reported for each app container must be the size it currently has in the cloud, not the size of the next backup as suggested in the Settings app.
If my hunch is right, my defect report here is not a Minecraft defect, but an iPadOS defect. I suggest we close this one, and I will keep an eye on this going forward and revisit this issue if I collect new data that points back in the direction of Minecraft.
Cheers!
Does MCPE-161293 describe your issue? I am not sure if the iPad has the exact same storage menu as the iPhone.