Did you scan a document folded in half whose paper size is A3, B4, or double letter size in a double-page spread?
Scanned images are merged automatically only when the paper size of the document folded in half is A3, B4, or Double Letter size in a double-page spread.
Perform one of the following:
Are there any characters, figures, or tables on the fold line of the document folded in half?
Scanned images are merged automatically only when there are characters, figures, or tables on the fold line of the document folded in half.
Perform one of the following:
Have you selected the [Merge both sides of an image] checkbox in the scan settings?
If you are performing a scan using a profile other than the profile that is linked with a cloud service by using ScanSnap Cloud, select the [Merge both sides of an image] checkbox in the following procedure, and then try scanning again.
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Display the scan window of ScanSnap Home on the computer.
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Select the profile that you are using from the profile list.
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Click the [Edit profiles] button to display the [Edit profiles] window.
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Click the [Option] button for [Manual Feeder] in [Feed mode setting] to display the [Feed option] window.
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Select the [Merge both sides of an image] checkbox.
Are you performing a scan with a document inserted into the manual feeder?
Scanned images are merged automatically only when a document is inserted into the manual feeder and scanned.
Insert a document into the manual feeder and perform a scan.
For details, refer to here in the ScanSnap Help.