AH, I think you are seeing this dialog, am I right?
That dialog is actually intended to alert you when an external change has been made to the config (for example you directly edited a config file in a text editor, or pulled in from GIT resulting in modified files inside your stack config).
Since in your case it was actually Indigo that instigated the filesystem-level change, you should not be seeing this alert.
However, by following your steps above, I was indeed sometimes able to replicate this. I have a feeling this identifies not one but three separate bugs, all conspiring against you in this scenario lol. Nasty!
I will dig into it. This won't be fun to fix, but if I'm right it will address the two existing intermittent-but-significant bugs I am aware of in Indigo. Thanks for the report!