Yes you can switch easily best is create a separate directory and install in it. You will have to modify (override) your configuration and provide for each pair the "BOUGHT_PRICE" that way it knows that what price you had purchased those coins for. Try and test with one pair and test and then migrate all other pairs. You can always switch back from 4.x to 3.3 anytime as you have the backup directory just run Gunbot from that directory instead and you are back on 3.3.
There is little test and configure that you might have to do but you can always review the original config.js file that comes with the installation and also a great configuration tool that one of the member has created which generates the configuration based on your input a very good GUI interface...
https://github.com/atomize/Gunfiguratoror
https://atomize.github.io/Gunfigurator/I hope this helps...
Good luck!