Not all menu customizations appear to be copied over on installation of CbB. Comparing their respective folders in SONAR and CbB, I see multiple .pgl files for SONAR but just the one default .pgl in CbB.
That would suggest that your menu layouts might revert to the default in CbB. However, that shouldn't affect the original files.
Have a look at the datestamps in %appdata%\cakewalk\sonar platinum\plug-in menu layouts. Those datestamps will reflect the last time layout changes were saved. If SONAR is open, you'll see a couple temporary copies (.tmp extension) but those can be ignored. None of the others should have recent dates - unless, of course, you've recently made changes to them yourself.