Thank you for your enquiry.
I wasn't able to replicate your issue exactly but it worked for me when I ran the tool again whilst having the 'Dimension In SketchUp' & 'Override Existing Scenes' fields enabled. Note: Sometimes the dimensions don't appear straight away but will once you click on one of the scenes.
Regarding deleting the scenes, how were you doing this (i.e. manually or via the 'Delete All' option in the Scene Tool)?
If the above doesn't work for you, would you be able to please attach a model with the issue so I can try & replicate the issue? Would you be able to please send over any error message that appears when using the tool (go to Extensions > Developer > Ruby Console, then copy & paste any message)? Thank you in advance.