[5.4.1] Updates Web Service Objects and causes 400 errors

Running 5.4.1 causes some of the Web Service Objects to get modified and causes 400 errors across all API calls. If the Web Service Object is opened many more lines are added to the file, but all of the files are getting updated/broken even without opening them. This is happening on both Windows and OS machines and we have had to revert to 5.3.1.

This seems to happen on machines that used the Import Settings option from 5.3.1. The one machine that imported settings from 5.4.0 seems to be fine.

Text added to API calls:

5.4.1

Many of our API calls are constructed dynamically, so the API objects only contain the authentication/header details. However, this seems to break our API calls across the board.

Even the qTest integration is having an issue on one machine (Windows Server 2016):
Unable to open qTest navigated test case.
Reason:
QTestIOException

Details:
no protocol: /p/44785/portal/project#id=12523602&object=1&tab=testdesign

Can you send me your project privately for investigation?

I’m sorry, but I cannot share our project, because of security.