After reading post 1-15, I think that you are overlooking the power of LR. All you have to do is process one photo in each folder that way you like it using Lightroom develop modules controls. Then save those adjustments as a preset (for future use).
Next, select all images in the library folder of which you are working, select sync, deselect all, then manually select only the processes that you made changes to, then sync across all images in the folder.
Repeat this for each subsequent folder.
To output jpeg files you will need to set up an export command for each folder once the processing is done. (File>Export, or CTRL+SHift+E) That's very simple to do.
If I've left any part of this unclear to you, ask and I'll add more info.


