I tried without /quiet first.  It was just a confirmation to overwrite.  It did not throw any errors.  Fully qualified path also did not work.  Frustrating.

Anyway, I just stripped out...

Ugh, this is getting weird.

So I ran this:

for %f IN (*.dtsx) DO dtutil.exe /file %f /encrypt file;%f;0 /quiet

It appears to have worked.  All of the projects now have the ProtectionLevel...

I am going to test this now.  When this was originally set up I believe encrypting the data was believed to be the best practice. But all of our passwords...