I just tested this issue in Studio One 3.5.1 and was unable to re-create it. Try creating a new song, load one instance of a Presence Instrument, and then add some MIDI notes. Convert to audio and check the box to "Preserve Instrument Track State." You can then right-click the track and transform to instrument. This should not create a crash. The crash may be caused by a 3rd-party plug-in. Try removing plug-ins and see if you can identify one that is causing the crash.
For general troubleshooting, try removing Studio One from the Applications folder and download/install the latest version from your my.presonus.com account once more. You will also want to try removing your settings files. Below are instructions:
Go to Help>Open Settings folder.
Copy the contents of the folder over to a folder on your desktop.
Close S1 and delete the contents of the settings folder with the exception of the user.license file as well as the "Extensions" folder.
Open S1 and go to Studio One>Options (Preferences on a Mac) to reconfigure your settings.
Test to see if the problem is resolved. If it is not, please feel free to copy your settings files back over from the backup that you created in step 2.
*If you are missing presets or Sound Sets after doing this, simply double-click one of your Sound Sets under Documents>Studio One>Sound Sets.
If the problem persists, please log a support ticket from within your my.presonus.com account. Just click the "Support" tab and log a ticket. When you do, please attach a song file that illustrates the issue with a couple of numbered steps.