I finally got the solution to this problem from the Overloud tech support. Just in case this happens to anyone else here is the solution that worked for me:
1) Open TH2 stand-alone
2) Press & hold for a few seconds the "Preferences" window, until a folder's window appear
3) Now close TH2 (but don't close the folder's window yet)
4) Remove the file named "preferences2.xml" from that folder's window
5) Now start SONAR and TH2 inside it, it should now have been reset to its default window size
Thanks, Scook for your efforts. Federico, from Overloud, provided me with the answer.