Sorry if I’m covering stuff you already know, but just to make sure:
The default behavior is not to delete posts when they fall off the feed, but to retain them. Under Syndication –> Feeds & Uploads –> Advanced Settings –> Feed Update Type, there is a setting to control whether FeedWordPress treats the feed as *Incremental* (i.e., retains posts whether or not they still appear on the RSS feed), or as *Complete* (i.e., retires posts once they no longer appear on the RSS feed).
Do you currently (a) have this set to Incremental? If so, then the solution should be to switch it to Complete and Save changes.
Or do you currently (b) have it set to Complete, but are finding that the setting no longer works as expected? If so, let me know, and I’ll take a look to see if I can figure out what’s going wrong.