You seem to be implying that you will be surveying current users for the current system, and this is likely to be problematic beyond the mere appropriateness of the survey questions.
A basic principle in research (which is what you are doing) is that, for a valid comparison of two things, everything else has to be the same other than what you are comparing.
In this case, you would want the same kind of users to test each system. The current user base will be experienced users with respect to the old system but brand new users with respect to the new system. The way they approach the two systems won't be at all equivalent, and thus, neither will their answers to the survey. Further, their knowledge of the old system will inform the way they approach the new one, which also invalidates the comparison.
Some of the potential consequences of this problem:
- People may prefer the old system simply because they are resistant to change.
- People may repeatedly make mistakes with the new system because they try to do things the "old way" and press the wrong buttons, etc.
- People may think the old system is a pile of garbage, preferring the new one simply because it is new and shiny--even if the new one is not really usable.
You will probably end up measuring things like people's resistance to change or how they feel about their job for the last five years, rather than comparing the performance of the two systems.
If you truly want to compare the two systems, the only real way for the comparison to be valid is to have completely new users test both systems.
If this is impractical (as is likely), a fallback option is to have existing users test the new system only. You will still have some of the problems of bias, but there are fewer consequences when you aren't making a direct comparison to the old system. And you will gather lots of useful information this way.