So that means I scrap the multiple versions of the toc file with this line
## Interface: 110000, 40400, 11503
Zip everything up and publish my distribution file. Joe user downloads it and copies it to his addons folder. The problem is the old _Mainline.toc file is still there so it gets loaded and the addon is now out of date because it still says ## Interface: 100207. Is there a way to deal with this or do I still have to maintain the various .toc files.
You can just have a single addonfolder.toc file with the multiple versions interfaces and all game clients will read it.
If you have seperate .lua/.xml files you want to use in differerent game clients then you will use the addonfolder_version.toc format, each containing the files for that client.
The no extension addonfolder.toc will be used where no addonfolder_version.toc file exists the client that is being loaded.
Clear as mud? 
If the code is incompitble then having multiple verion ID in the .toc it will still error. The ID are just for the not having your addon not show as out-of-date.
Thanks for the reply.
That all sounds how I was expecting things to work. What I was hoping to avoid was having to keep the multiple files.
If you downloaded a previous version that had the addonfolder_version.toc then upgrade later to a new version with only addonfolder.toc the old now unused file will still be in the folder. When you load the addon it will use the old file and it will show as outdated. It loads and runs fine but it will show out of date and you will have to check that box.
I was wondering if there was a way to delete or get wow to ignore those old addonfolder_version.toc files. Looks like I have to maintain them at least for now.
That’s assuming people just unzip over the top of an existing addon folder which should only apply to some people that manually download/unzip. Put a note on the download page telling them to delete the old folder first.