This should go without saying, but – Don’t delete anything until you are reconnected with your collection!
Did you check the links I posted? They explain which is the “current” location and which is the “new” location (ichi2.anki). A “parallel” install from GitHub will get you access to your collection at the “current” location. Then sync that to AnkiWeb. Then return to your primary install and sync to AnkiWeb. That will bring your data to the “new” location that Anki can access.
[If you want to have a better understanding of what is what in your Anki data folder – Managing Files - Anki Manual .]