this means it's just your VM that needs to be fixed).
If the scope is just your machine, consider just getting a new VM.
There aren't many hotfixes for platform since it is updated monthly anyway, but when there is it's cumulative and you install the whole thing at once as an update.
Even though you get the source you don't worry about it going into source control or building and compiling it, because essentially you have the binaries already in the update which is ready to deploy to other non-dev environments, and you always get the whole source anyway - as opposed to deltas of just changed objects.
I recommend a previous post I made on the topic of updates, upgrades and hotfixes.
This topic discusses the two methods of customizing source code and metadata of model elements - overlayering and extensions and details supported extension capabilities.
This means that the number of objects in a pending changeset for a prepare step could be LESS than the number of objects in a pending changeset of a hotfix.
A hotfix could technically also be adding objects, and new objects of course don't exist before applying the hotfix so they also wouldn't be in the prepare step. After doing the prepare option, you have to check-in the pending changes.
This is simple source control logic but many people forget this.
You want to check-in the original versions of the objects prior to applying the hotfix.