The Remove method of the NotesEmbeddedObject class always work for me. Do you save the NotesDocument afterwards, it is not showing that in your code sample.

Add a doc.Save() after o.Remove and see what happens.

I added a print statement just before the save, so I know it's saving each time.  This one really has me stumped - but I'm sure I'm missing stupid.

My code looks now like this...

I had the save command further down, but added it here to see if it made any difference.  My doc properties looked like this before I ran the code

The console shows the results...

but, when I check doc properties, nothing has changed.  It shows 5 SuppAttach fields and 6 $File fields.

I'm not doing anything to change the attachment type.  I'm just using the upload control "out of the box".

Print out filestr and see what the value is.   Also if you run the agent manually does it work?   Does the signer of the agent have the correct right?  sess.commonusername will signer of the agent

Thank you for all your suggestions - sometimes it just takes another set of eyes.... my script was working with two document variables and I was saving the wrong one after the attachments were removed. 

Rookie mistake, but apparently, I still need to be humbled after 15 years of development.