Website penalized for too many links from one source.

My boss's website where she sells mosaic tiles has a PR of 4 and her domain was created in 2007. Her site was doing really well for certain keywords like glass mosaic tile and related keywords. She only had like 30 or 40 unique backlinks awhile back.

Somehow, one of her website programmers put backlinks to her main site pointing from a sister site. I did a backlink check on her main site and there were thousands of backlinks pointing from her sister site. She took down the sister site but her main website lost its rankings for certain keywords and she is not making any business.

What can she do for google to realize that those backlinks are no longer active? I know she got penalized for having too many backlinks from one source and google probably saw that as spammy backlinks. But, now I am trying to save her site and bring it back to search engines. I told her it may take awhile for google to realize those spammy links are no longer active and told her to build quality and variety backlinks. But, since her sister site was taking down, those spammy backlinks are still showing up.