We use a number of Sales Pipelines. The settings for Deals affect all of your pipelines. For example, we use "Sync lifecycle stages to associated contacts and companies" which automatically turns a company to Customer after a deal is Won. This doesn't make sense for all of our pipelines, but we are unable to make toggle this setting without having it change for every pipeline in our database. We have pipelines for small, one-off sales, but these Customers are ultimately still a Prospect in our overall organization.
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