The current limitation affects both map interaction and attribute table behavior when working with large query results in ArcGIS Enterprise, including version 12.1. When using the Query widget with multi-page results, the map does not fully update beyond the first 1,000 features and continues to display only the initial set of records when navigating between pages.
As an enhancement, it would be beneficial for multi-page query handling to ensure that both the map and attribute table remain fully synchronized with the entire result set, rather than being restricted to the initial 1,000 features.