To workaround the issue in the interim there are a number of options available:
1. Do not use an array of composite types. Create a single entry for each item in the configuration. This way the other entries will not get overwritten.
2. Use string instead of securestring. However the content typically passwords will be visible so it may not be a good idea.
3. If you keep using the array of composite types configured as is you will have to type in all the passwords (secure strings). This way they will be overwritten with the correct information.