There is a way to do it in Illustrator by using the Variables tool. Essentially you separate them into single files, setup up a spread sheet with the file locations, setup a template in a single illustrator file and then import the spreadsheet and use an action to save each file with QR code and cut lines. There are tutorials on how to do it and the steps on YouTube somewhere, also guides in other places if you look up how to use Illustrator Variables. Below is my instruction list I made for myself when I did a bunch previously. It's not exactly worded for others to understand so probably best to follow instructions elsewhere. One thing to note is to use Google Sheets to make your .csv, as for some reason it wouldn't work in Excel for me when exporting the file. It takes some time to figure out the first time around, but then after it's much easier.
-Setup main illustrator file in Production folder J3679.ai
-Get list of source files in directory
*Use PowerShell to get a list of files in the directory w/path.
Get-ChildItem -Path "G:\OneDrive\Job Files\clientName\Signage\J3679 - QR Codes - 1000\sf" -Recurse | Select-Object FullName >filelist.txt
*add " " around objects when they have a space in the file path.
-Copy file names into google sheets database and download as CSV.
*Make sure to leave the @qr on the top line.
-Illustrator variables panel -> Load Variable Library choose the CSV database.
-Illustrator Actions panel -> Batch -> Convert to dir. Save as PDF
**Below is for setting up the files into batches of print files if you don't just nest them in your rip.**
-Combine pdf files for import into illustrator
-Drag combined files into illustrator
-Embed files
-Select all clipping masks and delete
-Arrange artboards for 24 lines
*check to make sure the height for files is correct.
-Select all and transform -> rotate 90°
-Move one item from each line and align the line straight multiple times
-Arrange lines with 0 spacing -> group
