If you have Yoast, upgrade to Yoast Premium to enable the built-in Redirect Manager. That way, if you do delete the Main Parent Category Yoast will HELP YOU by redirecting categories as needed internally if you ” break things.” Clearly, what you have described is not “ideal” but it also WILL NOT KILL YOU if you don’t add unnecessary sub-categories to your existing format. When we say “flat architecture structure” that doesn’t necessarily mean all one level. It just means, don’t push the content needlessly deep sitewide. Many many sites with your structure are doing fine. Just don’t exacerbate the problem by adding needless categories unless you have the content to support those categories.