The data from Choose Data section is inconsistent with application data for LQE datasource
2 answers
The data for Choose Data section when creating a new report is fetched from meta-model. The root cause of the issue of the issue is that your meta-model is not refreshed in Report Builder.
The solution is to refresh your meta-model according to How to refresh meta-model for the Data Source document.
In order to have up-to date data you need to refresh meta-model each time you are performing any modification in the project for the data which is designed to be visible in Choose Data section of Report Builder.
This technote should also be useful for initial troublshooting: MustGather: Investigating problems with wrong data available in Lifecycle Query Engine data source.