I actually just set this up for a client:
The parts I didn't share:
Variables.CreateNewList List=> FilesToMerge
SET pdfFilesPath TO $'''C:\\Users\\micha\\OneDrive - Peak Digital Transformations LLC\\Documents\\Clients\\Forge\\Audit\\Saved PDF Files'''
SET pdfFilesPathSchedules TO $'''C:\\Users\\micha\\OneDrive - Peak Digital Transformations LLC\\Documents\\Clients\\Forge\\Audit\\Saved PDF Files\\Schedules'''
SET pdfFilesPathNotes TO $'''C:\\Users\\micha\\OneDrive - Peak Digital Transformations LLC\\Documents\\Clients\\Forge\\Audit\\Saved PDF Files\\Notes'''
SET pdfFilesPathMerged TO $'''C:\\Users\\micha\\OneDrive - Peak Digital Transformations LLC\\Documents\\Clients\\Forge\\Audit\\Saved PDF Files\\Merged'''
Create New List -> FilesToMerge
Set Folder1 (I had it as pdfFilesPathSchedules)
Set Folder2 (I had this as pdfFilesPathNotes)
Set MergeFolder (I had this as pdfFilePathMerged)

So, this basically reads all the files from the first folder and only merges them if there is matching file in the second folder.
Hope this helps.
Here is the code for lines 6 and on...I don't want to share the folder variables...don't forget to create the list up front:
Folder.GetFiles Folder: pdfFilesPathSchedules FileFilter: $'''*''' IncludeSubfolders: False FailOnAccessDenied: True SortBy1: Folder.SortBy.NoSort SortDescending1: False SortBy2: Folder.SortBy.NoSort SortDescending2: False SortBy3: Folder.SortBy.NoSort SortDescending3: False Files=> Files
LOOP FOREACH PDFSchedule IN Files
Variables.ClearList List: FilesToMerge
SET PDFNotes TO $'''%pdfFilesPathNotes%\\%PDFSchedule.Name%'''
Variables.AddItemToList Item: PDFNotes List: FilesToMerge
Variables.AddItemToList Item: PDFSchedule List: FilesToMerge
IF (File.IfFile.DoesNotExist File: PDFNotes) THEN
NEXT LOOP
END
# If PDFNotes doesn't exist, skip
SET PDFMerged TO $'''%pdfFilesPathMerged%\\%PDFSchedule.Name%'''
Pdf.MergeFiles PDFFiles: FilesToMerge MergedPDFPath: PDFMerged IfFileExists: Pdf.IfFileExists.Overwrite PasswordDelimiter: $''',''' MergedPDF=> MergedPDF
File.Move Files: PDFSchedule Destination: $'''%pdfFilesPathSchedules%\\Processed''' IfFileExists: File.IfExists.Overwrite MovedFiles=> MovedFiles
File.Move Files: PDFNotes Destination: $'''%pdfFilesPathNotes%\\Processed''' IfFileExists: File.IfExists.Overwrite MovedFiles=> MovedFiles
END
Good luck!