I've checked the support FAQ, but find nothing about file maintenance dealing with links. Compact apparently re-indexes and compresses the FTM database. However, I have yet to find any method of checking links within the FTM file.
I moved a GEDCOM to FTM a few months back. The past month I began noticing linkage problems. Running a descendant report I found a 1950s member of one family listed as the father of a 1700s member of another family. This is the second time I have found such an error. And yes, I do routinely compact the file
Concerned, I exported a GEDCOM from FTM and into another genealogy software that does have file maintenance tools to check linkages. That software identified 77 additional linkage errors.
I like the interface and capabilities of FTM 2012. However, if I cannot be secure in knowing that my data is being maintained correctly by the FTM database (checks and maintenance of the database), the appearance and capabilities are of little value.