If everything is OK, you can remove the old folder and its content. Next, run the GUIpoint to the required Rom and disks in the new folder or where you kept them outside of the old folder and adjust the other GUI settings to match what you had before. If they are outside your old Basilisk II folder, leave them where they are now.
If you kept your Rom file and hard disk image s in the old Basilisk II folder, copy them into the new folder. The number of dll files may be a bit overwhelming, but the up-side is that it is no longer necessary to install the GTK development kit to run the GUI. Most dll application extensions files included are needed to run the GUI. If you are upgrading from an old version of Basilisk II, the best thing to do is to download all files into a new folder and make a fresh start but you can still use your old disk image and ROM.
