Would have to download the project in order to test the behavior here, but in general in Live, if you alter any element linked to automation within the arrangement view, automation will grey out and you will need to use the "Re-Enabled Automation" button to make them active again, it's kind of default behavior within Live I think.
Now if you did use the button once and then save afterwards, I believe that automation's lanes should not go greyed again when re-opening the project if you don't alter anything yet. Make sure to use the button before saving and save as a different project to be sure it's keeping the changes.
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EDIT : Well in fact nope, saving the project(s) under a different name, even using a new location folder and using the "Collect & Save" option in Live won't help, sorry. So yes, it's something I've seen a lot happening in Live, you'll have to use the button each time you re-open the project. Not sure if there's a setting to overwrite this, couldn't find any. Think this is coming from the fact that the historic of changes made to the project are somehow embedded in the Project file data, you can see this going to "edit" in Live's Menu.
Using MacOS High Sierra & Live 10.0.06 here & also tested under Beta 10.1 with the same behavior, have to click on the button each time