This is a real, important issue in enterprise-focused SaaS that sneaks up on your in Years, 3, 4 and 5.
You really can’t deprecate any features that are perceived as important to your core customers. The customers won’t stand for it.
Your biggest customers, in many cases, won’t really want much change, or often really, >any< new features. Not really. They’ll want to dial-in a business process around your product, and potentially, improve it later by selecting a subset of new features you add. But the last thing they want is to lose a feature they rely on. Period.
The reality is, enterprise-focused SaaS companies are very careful when they deprecate anything any material number of customers use. Even simply migrating them to a “better” version of something creates lots of stress.
There’s no perfect solution, but I have one recommendation. Assume you can’t really deprecate anything. At least, not anything more than 1% of your customers use. And whatever you do, don’t let deprecating be an excuse for not improving a feature. That can work in B2C. It doesn’t in B2B.