I concluded the bug was resolved in ME 3.7.0GA and just tested again on the latest ME 3.7.2 using the following process:
1) Created Java project, MyTestProject
2) Manually adding Ant builder named “TheCanaryBuilder” to MyTestProject from the Properties->Builders
3) Added web capabilities to MyTestProject (should add a bunch of ME builders)
4) Opened Properties->Builders on MyTestProject and observed that “TheCanaryBuilder” was still present. Then inspected .project for and confirmed presence.
Can you try this procedure and confirm/deny similar outcome as I report?
Here is a former thread for the problem reported before ME 2.7.0GA/3.7.0GA rolled out. https://www.genuitec.com/forums/topic/add-webproject-caps-deletes-existing-builders-closed/
FYI: there is a hidden preference that will instruct ME to append builders to builder list instead of the default prepend behavior. We are trying to position APIs to be available to other plugin developers to extend and modify ME behaviors.