IDFVersionUpdater can convert multiple files at once using *.lst file. Refer to AuxiliaryPrograms.pdf and search for section IDF Version Converter / Transition File Lists. If v8.4 files a.idf, b.idf and c.idf are in folder C:\EnergyPlusV8-8-0\PreProcess\IDFVersionUpdater, then 84to87.lst file should have the following contents

a.idf
b.idf
c.idf

Then IDFVersionUpdater should choose Files of type as Text File With List Of EnergyPlus Files (*.lst) and select 84to87.lst. check Create Intermediate Version Files if you want to save intermediate versions 8.5, 8.6 etc.This way IDFVersionUpdater should be run only once and there is no need to run various Transition-Vx-1-0-to-Vx-2-0.exeetc.

In general, the answer that Chandan is probably the best approach if someone has a bunch of files that they want to update to a newer version of EnergyPlus. If you want a script that can be run each time in a workflow, I would suggest a batch file that calls the Transition programs directly. Essentially, each transition program named TransitionVA-B-C-to-VD-E-F.exe needs to be run to update the file from one version to the next until you reach the version you want. The documentation on how to run Transition is here. It is important to have all the files in the proper directory including the IDD files for each version and the report variable CSV files.

I've done this in a fairly brute force way with Python. I'm sure there are better ways to do it. Here's the outline:

1. Use the glob module to find all the IDFs to transition, make sure to get the full absolute paths.
2. Use os.chdir to change directories into the directory that contains the transition executables.
3. Loop over the IDF files with a nested loop that loops over the transition executables that are needed.

Part of the reason that I did it this way was that I wanted the intermediate versions. If you don't, then this might not be the best approach for you.

You can open command prompt and create a text file for the .lst with all the file paths to the .idf files for updating. Navigate to the location you want the .lst Entering the following command to create the .txt list of .idf files:

dir c:\Users\path_to_idf_files\*.idf /s /b >list.txt

Open the .txt in the location to confirm the paths were properly formatted. Change the name of the .txt to a .lst file using the rename feature. Open IDFVersionUpdater and search for .lst files to open in the previous location. Run it. I did this recently for about 120,000 .idf files. It takes a while to run that many through the updater.

Run this Python script to create a list of all IDFs in a folder (that you want to update):

import glob, os

f = open("update.lst", "a")
for file in glob.glob("*.idf"):
    f.write(f"{os.path.realpath(file)}\n")

f.close()

Then, use the IDF updater and select the update.lst that you just created.