I have the same issue... Any news regarding this?
To reproduce;
1- Create a custom visual in using https://app.powerbi.com/devTools
2- Export custom visual as a pbiviz
3- Open PowerBi Desktop, import a dataset
4- Import the pbiviz
5- Save and close PowerBI Desktop
6- Update custom visual in using https://app.powerbi.com/devTools
7- Export new version of custom visual, overwriting the pbix
8- Open PowerBi Desktop with the pbix saved at step 5
The viz in the pbix is still the previous viz from step 4. Reimporting the pbviz again, does not work, the viz is still the old one, not the new one from step 7.
This means that any pbix containing a version of the custom viz will not be updated with new versions.
A- FOR TESTING: As we must spend time reloading the custom viz in an empty pbix, and recreate a test report each time. We cannot simply have one test reports, just reload it, update the pbiviz.
B- FOR PRODUCTION: pbix build using a custom viz will be stuck with that version. Updating to a new version of the pbiviz will require a complete rebuild of all the reports from a clean, data only pbix.