You’re right that it’s not the plugin that’s changed; it’s SonarQube.
In 2025.1 we store measures data a little differently for optimized DB usage, and under some circumstances, we’ve realized it can affect the UI with slow loading times if the Dependency Check plugin’s HTML reports have been stored as well. So in the point release, we added this warning.
As for how you should deal with it, you can choose to stop uploading the sonar.dependencyCheck.htmlReportPath. Or you can ignore the warning and any UI slowness.