The way the Internal Link Juicer works is to not persist links in your content (nor manipulate the content of your site in any way). With that, you cannot do anything wrong – because after you decide to uninstall the plugin your site will be like it would be without ever using the plugin.
This approach brings maximum flexibility for you to test things, switch options, and so on and so you can always rely on the Internal Link Juicer will only link stuff that you have configured. If you change your settings, your links will also change. So this behavior is intended.
The big deal of the Internal Link Juicer is, that it does everything on high performance without causing you any kinds of additional loading time (so you are good to go to just let it be installed and get used to all its fine-tuning features to level up your internal linking process).
