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I have a few thoughts for you. First, it may take time. In many cases when a penalty is lifted it can take 1-2 weeks to see the benefits of the penalty being lifted. Second, this is probably obvious, but is the brand name relatively unique? In other words, if your brand is a common word or a keyword, then you may not see a return to good rankings. Google may decide that when people search for that word they're not necessarily looking for your brand. Next, it's possible that the site is trapped under Penguin and you need to wait till Penguin updates. With that said, Penguin doesn't usually affect brand terms too heavily, unless, again, the brand is a common keyword. " Since uploading the disavow file, our homepage does not show up at all for branded searches. " - This doesn't sound normal to me. You should not lose rankings after filing a disavow unless you have been extremely aggressive and disavowed really good links. Even then, it takes a good amount of time for the sites in your disavow to be recrawled and the disavow applied. So, if your drop happened shortly after filing the disavow it could be coincidental. There have been a LOT of changes in the SERPS recently and it may be that your site is one of the many that is seeing wild swings. With all of that said, there are cases where Google makes mistakes. I've had a few cases where I just couldn't figure out why a site couldn't rank for their brand name. Here's an example: https://productforums.google.com/forum/#!topic/webmasters/VFnodOiYXqc;context-place=topicsearchin/webmasters/pedorthic. In that case we were able to get a Google employee's ear and magically, after not ranking for months, the brand terms were back within 24 hours. But, this type of situation is likely quite rare. I am guessing that in your case, you need to give it a bit more time. Best of luck!