Keep the wrong things out of a download

Three of the limits on what a download can hold have a habit that avoids them. Each takes a moment while you play; none can be repaired afterwards without a cost.

Keep one download to one world

Stop the download before you travel to a resource world or a plot world of the same kind as the one you are in, and start a new download there. Why the two would otherwise mix into one folder is covered in two server worlds of the same kind.

Dismount before you travel between dimensions

A mount you leave behind on purpose is saved once, in the dimension it is actually in. To clear an extra copy out of a download you have finished with, open it in singleplayer and kill the leftover mount. That tags the download as opened in singleplayer and blocks resuming it, so leave it until you have downloaded everything you want. The mechanism is in a mount you ride between dimensions is saved in both.

Leave one item inside an entity container

A single item is enough for the download to see real contents and replace its stored copy with them, so the save holds what you can see in the container. That does not get you a container saved genuinely empty: if empty is what you want, empty a Minecart with a Chest, a Boat with a Chest, or a chested animal before you start a download rather than during one. Why an emptied one keeps its old contents is covered in a Minecart with a Chest you empty keeps what you took out.