When you use Batch Tasks > Perfect Match to apply from an original translated document (with confirmed segments) into a document which isn't entirely new (in this case some segments are blank but with AT as the status) then those segments are not overwritten. Having checked with support this is by design:

"If the files to which you are applying PerfectMatch already have confirmed or edited translations, they will not be overwritten. PerfectMatch will only overwrite the target content if: 
The target has a status of Not Translated. 
The target is a copy of the source and has not been edited manually or confirmed. 
A segment in the project file and corresponding segment in the bilingual reference file will only have PerfectMatch applied if they have identical tracked changes in the source. 
No PerfectMatch will occur if one of the segments has tracked changes in the source and the other one does not "

But in reality this seems counter intuitive since Perfect Match is considered the gold standard of a match and should take priority over anything that isn't a locked segment or already perfect matched. So my idea is that Perfect Match, when applied should overwrite everything.