Now is the right time. It is rarely too soon or too late to make life easier for the people who rely on you and your products.
People do adapt to complicated systems, processes, and interfaces. Most people are more comfortable, in the immediate term, when things feel familiar. And as you say, people will often be confused, or even frustrated, if you change something they’re already familiar with. But this doesn’t mean they find those things intuitive and enjoyable to use or follow. If you’re looking to improve the experience for new users and retain users for longer, I strongly recommend taking informed action.
I recommend you conduct a tree test of your existing IA (tree) to find out which labels and hierarchy people find confusing (evil attractors) in a task based context.
After you’ve completed this benchmark tree test, conduct a card sort to find out how users want your content to be organised. You might find it useful to conduct card sorts with both your experienced and inexperienced users, and to investigate any differences.
And then before you restructure the navigation or rewrite the content, I recommend conducting another tree test using a new tree and the same tasks. You can now compare the results of this second tree test to the benchmark test you've already done. Go ahead and iterate your tree until you're happy with the results. This will give you the quantitative data you need to convince those around you that the changes will work.
You need to invest time into discussing the changes with your users. Besides ensuring a worthwhile outcome, involving your customers in this journey will help them understand why you're making the changes and reduce the impact of change resistance for the sake of it. In my experience people usually welcome change when they feel valued.
Conduct in-person user tests after you’ve implemented the changes. What you're looking for here is confirmation that your new IA works in the context of the wider application aesthetic, and with real content. I expect you'll also pick up some useful and subtle ways to help you communicate the changes most effectively.
All the best for your research and design!