I have to start my downloads from scratch
Your downloads should be safe, unless you delete
everythingbefore installing a new version.
Your downloads are in your home directory (places > home), and they will still be there if aMule will not run.
You cannot see them yet, so in your home directory go to "view" > show hidden files
Then you will see lots of folders, including a ".aMule" folder.
Inside that folder there are 2 more folders.
In "Incoming" you will find the completed downloads.
In "Temp" you will find the not yet completed downloads.
If you want to deleted aMule, you can simply secure those files by copying and pasting all of them to a new folder
in your documents folder, for example. So that when you have a new aMule, you can restore those files.