Color management and batching?

The javascript for an assign and convert is fairly simple. This one would ask for a folder of scans to batch. Note that the profile names have to be exact. Also, I‘m doing a simple Save, if you wanted a specific file format we could include some save as options

#target photoshop
var psdFolder = Folder.selectDialog("Select the folder containing scans", "");
var myFiles = psdFolder.getFiles();
app.displayDialogs = DialogModes.NO;  
for (var a = 0; a < myFiles.length; a++){
    try {
        var d = open(myFiles);
        //assigns profile and the convert. IMPORTANT, the name strings have to be exact, 
        //i.e. it's "Adobe RGB (1998)", not "AdobeRGB (1998)"
        d.colorProfileName="Fuji_Frontier-Scanner_V3a";
        d.convertProfile("Adobe RGB (1998)", Intent.RELATIVECOLORIMETRIC, true, true);
        d.save();
        d.close();
    }
        catch(e) {
        continue;
    }
};   

Don't rely on the "missing profile" dialog (which gets suppressed anyway). Use Edit > Assign Profile. Then Edit > Convert.

Are you sure the colors in the document without a profile that come from the scanner contain the scanners profile colors  you assign the document to before converting to Adobe RGB?  Try changing the assign to assign sRGB before the conversion, see if the colors are better then,