The difference here is that the files aren't on Apples servers, they are on your phones internal disk.

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This is about files that are on iCloud servers. Specifically, some photos on iCloud servers don’t get properly flagged for deletion when the user requests it. Something was getting corrupted.

Apple fixed the corruption issue, so now a handful of photo files affected by it appeared to rise from the dead. The files were always there in the cloud, but something like a corrupted DB entry was hiding them from view. Users thought they were deleted, but they were in some sort of corruption purgatory. Not visible to the user, but still taking up storage space.

Once the corruption issue was remedied, the photo app recognized the files, didn’t realize they were previously flagged for deletion, then started to sync them to the device. AKA, download them.

And yes, you can run third party software on Apple’s operating system. There are quite a few third party apps for managing iOS and MacOS’s file system.

Big complaint isn’t a lack of 3rd party apps, it’s that it’s hard to side load apps that aren’t signed.