Any time you upgrade Toolkit you need to also update the APToolkitNET.dll to ensure the version you are using matches the installed version of Toolkit. If it does not, this has been known to cause a variety of odd issues. In your particular case, the versions are far enough apart that it probably wouldn't work at all.
1. If the new version is installed you must update your references to match the installed version.
2. You should only ever have one version of Toolkit installed on your server. They use many of the same filenames and cannot co-exist on the server without causing problems.
If you MUST support both versions, you can copy all of the Toolkit files from the Toolkit Bin directory into your applications Bin directory. However, please note that this will ONLY work with .NET applications, this still requires a valid license on the Server for both versions of Toolkit, Toolkit cannot be installed on the server normally. So you'll need to install it on a server first to gather the files you need, then copy those files over to your application bin directory.