One night I got a panic call from a well known web designer who created open templates one of which I used. He said that because of the link at the bottom of his templates and the shift in Google strategies, the links now cause Google to penalize his site. He said that he did some research and that if I were to break the link and leave the mention as is without the link, he should be okay. I of course obliged. I also kept in touch to see how things were going.
I did some of my own research and this is what I found that fits your situation.
If your link pointed to a specific page and you changed it to the home page, you just made things worse. Sorry. Google specifically looks for large numbers of links to the domain root only. It is a sign of a low quality link and a potential link scheme. If the link had gone to a series of pages, then it would be seen as having a greater value. However, I would assume a small series of pages with a lot of links from the footer would equate to nearly the same thing as linking to a domain root if great enough.
Google is aware of designers gaming the system by creating links in the footer of their design and asking that the link remain. This was a widespread practice. Personally, this is the right thing to do. Tradition dictates that we give a credit to those who have helped us. But with so many designers and so many links, Google says this as a linking scheme and targeted these activities directly as part of their clean-up effort.
Keep in mind that designers were actually the least of Google's problems. SearchDEX created, using a bug in the footer of an extremely large number of valid and junk sites, links to it's customers sites and created link juice for keywords both appropriate and inappropriate for the target site. J.C. Penny was de-listed along with other major corporations from Google as a result. A well know article written by The New York Times told the story. SearchDex was not the only one. Because of this Google had to do something about links in footers, sidebars, and headers that were unnatural.
Citations count very nearly as a link. Google mentions this and it makes sense in today's search market. This is the reason why the designer who called me asked me to break the link but leave the credit. It would not violate Google's webmaster guidelines and was alluded to as a solution to links in the footer. And it seemed to work. In fact, I had links in my footers to my other sites where pieces were borrowed from other efforts. I changed these quickly.
It may be best that you break your links altogether and keep the citation. I think it all depends upon how may sites use your designs and large they are. If you keep links in the footer of your design templates, then link directly to a page for the design. If you do not have one, make landing pages for these designs. Personally, I would not take chances on this and create a citation instead to be safe.
I have no experience with this issue in particular with no-follow. That may be appropriate too. I am not sure.
Now to answer how long it will take to work out. Plan on 30-60 days under normal circumstances. It can take longer or less time of course. It all depends upon freshness of the various sites who are using the design. However, the 30-60 days margin does seem to about right most of the time. I would do the work you decide to do to fix this problem and just be patient. There is actually no drop in rank for this. Just a drop in the SERPs which should return to normal when the changes are noticed and worked out in the various systems within Google.