作者さんから早くも返信です

Hello,

IMAP is designed to synchronize two-ways, so deleting a message somewhere will delete it everywhere. This is just how IMAP works.

What you can do is hide messages instead. Note that you can set the swipe left/right target to hide.

Kind regards, Marcel

簡単に言うと双方向同期の設計の為、仕様ですとの事です
文面から見るとその点は変更しないよって事だと思われます