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Photoshop CS6 Export Multiple Layers with Fixed Top Layer Effect on All

I am trying to Batch Export 200 Images as PNG each with a Top Layer which has Glass Type effect. I actually have 3 different effects and 200 images = 600 unique exports.  
Effect + Layer (1-200)

Using "Files |Scripts | Export Layer to Files"  Turns OFF this Top Layer and only the original images export. This process also takes forever and should be done on subset samples eg 3 images. The PSD should also be saved prior to execution

By making "Comps" it was possible, but still a manual update and individual comp files for each export The need to apply to each comp is cumbersome also, although the exports work "File | Scripts | Layer Comps To Files.."

Should unique each export be managed as layers in groups? eg Effect At Higher level than group or should all related effects and images be located as a group?  The main idea is to change the effect once only to enable changes to all subsequent exports.

Should it be 3 separate PSD projects for each Effect Type?

The Process should be repeatable and minimal effort to update the 600 images. It would be good to know how to STOP the prefix as the files should be named from their layer comp name only

The files should take on their existing name based on their layer name.
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Scott Fell
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Scott Fell
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Hello Scott.. thankyou for your time...PC... I will take a look at your suggestion and provide feedback
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Hello Padas, thankyou for your feedback on this one.  It is a valid method but is not suitable in this case. It runs too slow with so many images.  I will now seek a solution in firefox using JSF to open and add layers for merging.  This will be a new ?
If you do this a lot, another option is to install http://www.imagemagick.org/ and you can do everything on the command line or crate a vb script.  I have this on my web server and manipulate images in bulk using image magick.
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Hello Scott,
pls note I did eventually solve it using Fireworks but thankyou for the link and post question support.
To achieve the goal one line of code is required in a JSF Command File for each effect.
fw.getDocumentDOM().importFile("file:///D|/Effects/MU.png", {left:0, top:1, right:0, bottom:1}, false, 0, false);

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This file is the 1st stage in the batch process prior to 'Export'
It simply opens the required effect layer prior to loading the image and exporting it.
I repeat the process 3 times for 3 effects.
The Batch Process may also include a 'Resize' and 'Rename' after the 'Export' process each time also.
The complete process for 1 effect and 260 files each 2485x1536 is around 8 minutes.
If an 'Internal Error' dialog appears as it did once for me, I just clicked OK and the process continued without issue.
After the native resolution files are created then the script can be run with just Export, Resize and Rename to achieve the required resolutions with new size suffix.
The entire process for 720 images is now less than 25 minutes.