Most likely: not possible.
but I am unable to re-generate from source
In other words: you can't compile it as a "project". Thus you lack the essential tooling that such a project definition comes with (like: easy access to "usages", and easy refactoring).
Let's assume for a second that you somehow manage to compile that one Enum java file into a class file. When that works, of course, you can go in, remove the corresponding constant, build a new .class file, and manipulate your existing JAR file to make use of that.
But the big downside is: you have no idea how many other classes are using that specific constant. Maybe, using javap and grep and whatnot, you might be able to identify usages of that constant. But alas, that doesn't help. Because knowing that some class uses enum E.y doesn't tell you at all how you would have to manipulate that class so you can remove E.y safely!
On the other hand, you assume that this change will cause a large application to somehow avoid unwanted behavior. Conclusion: there seem to be many many usages of that constant. What do you think that code should do then in the future? Sure, switch cases just don't executed any more. But what about method invocations that pass your constant as argument?! And worse: what about "clever" people who used the ordinal() method with that specific enum, or reflection (to create enum constants from raw strings coming from God knows)?!
Long story short: sure, theoretically, you can drop an enum constant easily. But most likely, the result of doing so will not work reliably.
Instead: step back. Don't look at your application in terms of classes and heck enum constants. Think about its features and modules, and rather identify which "whole components" can be safely cut/replaced from/within that system.
