No. Since Version 3 is a new and separate program, it will install and run with or without Version 2 on your system. None of the files are shared. You can run both programs for as long as you like.
Note: If you have Study Notes or verse additions to the Treasury, your older Version 2 files will be found when installing Version 3 and converted or saved in your new 3.0 directory. We recommend you make a backup copy of any important files, such as your Study Notes, before installing Version 3.