Unfortunately you've entered a limbo zone. Ancestry.com and FTM synchronize for the most part, but they don't synchronize completely. That means that whenever a sync breaks, you're going to lose something--either from Ancestry.com or FTM. In your case, it sounds as if you've uploaded a new tree to Ancestry.com from your tree in FTM 2012. This means that you preserve everything in FTM but lose everything at Ancestry.com that doesn't sync with FTM 2012.
If you'd posted about your problem before breaking the link between FTM 2012 and Ancestry.com, we might have been able to avoid your current predicament. Unfortunately, by de-linking your tree as you did, you've now crossed the point of no return.
If you delete the old tree from which people copied your media, then Ancestry.com will no longer indicate your tree as the original source. Your fix for this is to download this tree into FTM. The downside is that you will lose everything in FTM that doesn't sync with Ancestry.com. (That may mean nothing or that may mean the loss of many hours of work.)
Finally, no it doesn't matter that you leave FTM open all of the time. It certainly doesn't affect your ability to sync.