tonire To get this right so you are using EWS script to take actions on emails received on PF A "delete & move", PF B "create new item", PF C "create new item", If I get you correctly the issue is with deletion process which made Folder A a giant one but why isn't PF B & C are giants since all of them are having same input "email items" with same size?
one more point have you modified DefaultPublicFolderDeletedItemRetention across the organization (least value is 1 day) or even across that PF A "RetainDeletedItemsFor" (you can specify zero days here) where deletions are taking place to ensure that these items are always purged constantly.
Can you share with me your request in a DM?