Hi,
To me, your sales order might have got Manual pricing and would have passed on to the invoice as it is. Now, that when you clicked on the Update pricing - New pricing would have hapenned and hence the manual pricing would have disappeared.
To fix this error please use the Update Pricng option as "G - Copy pricing elements unchanged and redetermine taxes" OR "C - Copy manual pricing elements and redetermine the others"
Please let me know for any further clarification.