Batch Merge Files Into Single PDF

Yes,

use "Advanced > Document Processing > Batch Processing" for this:
1. Select "New Sequence > Select Commands... > Insert Pages" and configure it as you like.
2. Then choose "Selected folders" for "2. run commands on"
3. Click on "Browse" and select the specific folders for your sequence.
4. Then select the output location and press "OK" to save you batch sequence.

I did that but that just converts each page in each sub folder, but i need it to then merge each set of single pages into separate multi-page PDFs for each of the subfolders

I would like to know how to do this too, any help would be greatly appreciated.

"Insert Pages" needs an open PDF into which the other files are inserted.
You may find this open PDF needs to be in a location other than within the folder that is in focus of the Batch Sequence.
Perhaps using Create PDF > From Blank Page could serve as the open PDF. Delete the page when done.
All files (PDF or those of a file format supported by Acrobat for conversion to PDF) will be inserted into this open PDF.

Result of a trial using what radzmar suggested:
One PDF with continguous pages of content. File types inserted where PDF, DOCX, PPTX, and XLSX.

As to retaining the subfolder name, you may want to use the Search Forums feature to query the JavaScript Forum.
I seem to recall that this has been discussed there.

Be well...

I seen this question before and have used a Perl script to combine two or more pdfs into one document. I havent tried the batch merge, but found on a per need basis this works well.