If the people are still there, you've just detached a branch. Often this happens when you see a duplicate person and try to delete one of them instead of merging; you end up deleting the person through whom the branch was connected to your tree.
It's pretty easy to correct, just re-attach the key people (if your grandmother is missing from your tree, just attach her - if it's her parents that are missing from your tree, re-attach them. Everyone else will follow automatically).
You can do this in either FTM or on Ancestry.com, just do ONE of the following, then sync to fix it on the other tree. Note that these articles talk about how to DETACH and how to REATTACH. Your people are already detached, so skip to the 2nd part of the article: