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Once you have manually operated the top you have to reset the tonneau motor. First you have to push the red lever in behind the rear seat- you most likely had to pull this out for manual mode. Next you need to remove the passenger side trunk panel and push the motor back into position. The motor is near all the gearing on the passenger side trunk area and the body and presses in towards the center of the vehicle.
The check latchs message could be coming on because manual mode doesn't allow the rear latchs to engage and will chime the warning.
Please note- there is a very expensive motor and gear assembly that fails on these cars. An update is available that may save the motor assembly, but generally they don't work.
There are a number of items that can cause the "check soft top" message and the top not to work. It will need to go to a shop that can read the fault codes and signals that are missing for the top to work properly. You can expect 1 hour diagnostic time for a saab specialist, and I only recommend a saab specialist for this top issue.