We've been rolling along with all of our projects using the default issue type scheme. If one project wanted to add an Issue type, they would get agreement from the other projects and add it. No problem.
Now we have a new project. They want new issue types (that no one else wants) and they do not want to use all of the existing issue types being used by other projects.
No, I think you're doing the right thing.
Your "General issue type scheme" decouples the existing projects from having to accept new issue types being added to the system, and protects them from the new scheme(s) you want to create for the new project. It is a bit of a slog to swap them over to the new General scheme, but it's a one-off that gives you more freedom in the future.
The one thing that you have got slightly wrong, but is absolutely the right sort of thing to worry about is the indexing. Indexing never sends emails, as it's rebuilding an index, not changing anything, and it's changes that send emails. In this case, you don't need to worry about it at all. If you change the issue type scheme and the change has no effect (i.e. the new issue type list includes all the old ones), then there's no changes to the issues, so there's no need to reindex at all.
So, I'd say, go ahead and do what you suggest. There will be no emails, no need to re-index, it's just a change of config to help you out in the future.
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