Usually when you update your disavow file, you'll see a message in Webmaster Tools that looks like this:

 

 

However, quite often I have seen it happen where a disavow file is updated, but no message appears in Webmaster Tools.  Does this mean that the file was not properly uploaded?  Can you be certain that your new disavow file will be used by Google?

John Mueller said in a recent Webmaster Central Hangout that this is a known bug.  Start watching at 6:47:

 

 

Someone mentions that they uploaded a disavow file but did not see a message in WMT confirming their upload.  John Mueller responded saying,

We noticed this, looking into the disavow tool, that sometimes when you uploaded a file we didn't send a message.  We're still looking into where exactly these messages went internally but essentially if you uploaded a disavow file and you see that the status is updated in the disavow tool then that's fine.  You don't necessarily need a confirmation message in Webmaster Tools.

 

So, it looks like it's a bit of a bug.  If you've uploaded a new disavow file and you don't get a confirmation message in WMT it's nothing to worry about.

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