Hello,
Please have a look at the topic in our FAQ "How do I access server side folders?":
https://www.aqua-mail.com/?page_id=227So you could on some occasion sync a Folder and later un-sync it to remove it from Aqua Mail and vice versa.
You can also decide to simply "hide" the unneeded emails. To do that long press on the account in the main screen and choose “Options and Folders”, then “Account options”.
Tap “Deleting messages” and choose “Hide in the app, keep on the server”. This will change the default action icon for deleting messages from this account to “hide”.
Hidden messages can be restored by using the menu in the message list view. They will be also automatically deleted from the app at a later point to reclaim storage space.
Note that it’s not really necessary to delete messages from the app — old messages are automatically deleted over time without affecting the server, keeping storage usage under control. The default is to keep 250 most recent messages per folder (and can be changed in each account’s Folders and Options as “messages to keep”, renamed as “messages to cache” in 1.4).