Sometimes the simplest solution can solve so many little frustrations.
In this case, I simply wanted to see the hidden directories when selecting a directory in an application.
After a quick search, I realized that it was not a preference to change in the Finder but that I could simply press Command + Shift + . and see all the hidden directories in that window.
It allowed me to select a new JDK and tadam, my project is back to working.
