I’m not sure what you mean by this but I will try to explain the Anti-Malware Quarantine in the hope it will better answer your question.
There is no “quarantine folder” actually, but the “View Quarantine” option on the Anti-Malware menu will display a list of files that have been found to contain malicious code and already fixed. The malicious code that was found and removed has been stored in these record in your database where it is safe and cannot be executed. I think the description on that page says it best:
The following items highlighted in yellow had been found to contain malicious code, they have been cleaned and the malicious contents have been removed. A record of the infection has been saved here in the Quarantine for your review and could help with any future investigations. The code is safe here and you do not need to do anything further with these files.
If you have cleaned some files that have then been re-infected again then you will also see this message:
The items highlighted in red have been found to be re-infected. The malicious code has returned and needs to be cleaned again.
There would then be an option on the page to “Re-clean the re-infected files”, which is highly recommended.
There is also an option to select all records and delete them from the Quarantine, which is not recommended at all. These records can be very helpful to keep, especially if you are still working to remove more infection and patch potential vulnerabilities. The information in these Quaratine records can also be very helpful for any further investigation into where the hack came from and how it might have gotten onto your site.
Please let me know if I have missed your point here or if you have any further unanswered questions that need more elaboration.