I am not aware of your specific situation, but not entirely unaware of
large enterprise application redesign situation either.
Based on my experience I would recommend steps to be taken
1) Find out what's wrong
Do an extensive research on what is wrong with current design. Do an objective analysis of your findings and clearly list down the gaps in your current system vis-a-vis expectation of your end users. Clearly underline and understand how your current system is not in synch with end-user goal, business goal or your buyer's goal.
2) Take business's feedback
Once you have developed some understanding of what your system should be, try and ensure that it is in synch with your boss's (boss is a short form for your management here :)) understanding as well. Ensure that your boss understand the gaps you have identified and take his feedback on your analysis of his feedback as well.
3) Take your end-user's feedback
Your end-users, who have been using the current system for ages, must brace for whats coming. Biggest challenge for them is going to be change, specifically change in mindset. Idea behind this exercise is not only to find out what they think about the current product and validate your findings in step 1, but also to somehow get an idea on how to sell version-2 of this current system.
After doing these steps, you will be in much better position to take an informed decision on redesign.
So, to answer the specific question
a redesign without proper thought, especially in an enterprise
situation, can have serious negative consequences that have huge
1) Change for your end user, single biggest concern which can make or break your product. If there is a significant change in UX, plan and budget for this change management as well.
2) Gaps in understanding of your buyers and your own business, leading to change in buy/sell decision.
3) Change in your product image/perception unless it is thought through well. For example, if your product was perceived to be flexible and if your approach is changing, then plan and rope in your marketing department for the same.
4) For your own organization, you need to have a team what will support previous version and still keep working on new version as well. It is not as easy as it sounds.