Hi,
First, if you actually deleted the message from the server, the app may not be able to complete its loading (messages are loaded partially when checking mail). There are settings in the app, in Extended mode (top item) to load more of each message as the app checks mail -- there is an "unlimited" option there too.
Second, there is also a setting (under "Message display") to "allow actions with incomplete messages". The app will ask if you want to reply / forward a message it could not load completely.
Third, if the message is there on the server, but its position in the server's message list significantly changed because you deleted many (dozens) of messages using another mail app -- there is a per-account setting you may want to adjust so the app "looks harder" when trying to locate those messages on the server.
Long press the account -> Options and Folders -> Extended mode -> scroll to POP3 and increase "Message locate limit".