Forked module modifications, overwritten by Introjucer

Just had a minor disaster - I've forked the dRowAudio module and modified the local copy in my project folder. Updated the .git remotes etc to point at my forked repo. All been going fine, until I decided to update Juce and then had to update dRowAudio module too... had something unexpected when I saved the project which I now understand was Introjucer overwriting the module folder.. as I have now seem to have lost quite a few hours of work as I had not pushed my changes to my forked branch.

I guess I needed to be modifying the main copy and not have a project local copy of the module? Is there a more proper way to do this? (I don't want to add the module to my project repo)

It would be good if Introjucer checked if any files were different and gave a warning before overwriting..


Ok was not as bad as I thought... didnt lose too much (had pushed to Git not long before). 

Lesson learned - I am now working with the 'parent' copy which Introjucer can see. 

Are you actually saying you let Internet interact with your local copies before backing them up?!

I assume you mean Introjucer, and not Internet... and yes I did, without realising that Introjucer alters local copies of modules as well as components etc.