I think it could be done in PT3.
Here's my idea
I am aware that the tourney number is probably unique key in the database. If the key can be changed to look at 2 things it can be done. All normal mtt's shut be imported as normal but with a extra flag. Entry1. That's the new unique key. The normal mtt's never would have a second entry so this does not effect the anything else.
PT3 has to look for the word Entry in the name of the handhistory file. If i enter 2 times a multi entry Mtt i get 2 different HH.
FT20110126 $66,000 KO Guarantee (214518551), Entry 1 - No Limit Hold'em
FT20110126 $66,000 KO Guarantee (214518551), Entry 2 - No Limit Hold'em
So if the word key word in the HH is
Entry pt3 has to treat every entry als it own mtt with own mtt results and hud. When pt3 imports hands it first has to check the name of the HH file. If the name is entry 1 then it should be marked as entry 1 in the database when importing the hands. Like a flag and all hands from the HH with the name entry 1 shut be auto import to this mtt.
When entered 4 time the same thing shut be done. Pt3 has to check if the name of the HH contains entry2,entry3 or entry4 and post his the mtt number with its own flag in the database.
So first query if the name of hh file already exist in the database if yes then imports in this mtt if not mak a new record with flag entry2 ,3 or 4 and then import.
The summaries shut be imported to all entries.
Much nicer would be if full tilt writes the information in the HH itselfs.