What version of SalesCQ are you running? How did you transfer the prospect to a quote? Where were the notes entered?
I tested with version 8.1C (121012) and all notes and alerts were moved from the prospect to the new customer, whether I simply transferred from the Edit Prospects screen, or created a new OE order from the prospect quote on the Edit Quotes screen.
Of course, if you meant that the notes entered directly on the quote did not go to the customer, then that indeed is true, nor does Order Entry currently support notes on orders. If this is your situation, then you would have to extract the notes from the quote(s) and import them to the customer. There is no Export Quote Notes process, so they would have to be extracted in a different way, such as GridView or perhaps printing the Quote Notes report to an Excel file (and layout re-formatting would be necessary).
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Regards,
Softrak Tech Support