Rebase simply means that I am taking a version of the mod based on a specific version of the game (such as 0.12), and I'm changing/updating that base to the new version (such as 0.13).
It allows versions of the mod intended for older versions of the game to work on newer versions without affecting any changes made in the newer version, but does not add anything new for the new changes.
For example, if the v0.12 version of the mod is installed on a v0.13 game, the v0.13 content will likely not be accessible, some image errors may occur if they were renamed/moved, and/or bug fixes will not be applied. During a rebase, the changes that the v0.12 mod made to the v0.12 base game are simply copied and applied to the v0.13 base game.
Note that when I rebase a mod, I don't completely check its functionality. Most of the time, I only check that the game launches and nothing else. Since rebasing mods (at least for this game) only take a few minutes, I don't review every change, but if your saves work from one version to another, it's very unlikely that any issues will occur.