There have been a number of bills floor action on which has been governed by a unanimous consent agreement stipulating that all or some specified amendments will be need a 3/5 majority to pass.
The purpose of such a UCA is to expedite a bill that both parties want to see passed within a given period.
The Senate GOP want as a matter of partisan imperative to kill the health care bill. The slower the bill's progress, the more chance it will bog down completely.
So the suggestion that the Senate bill is safe from Stupak (as made here) makes no sense: there probably aren't 60 votes for Stupak, but there probably are 51 (or whatever simple majority is required - no doubt a number of senators will conveniently have other priorities on the day).
Of course, Harry could always try to organise a filibuster against his own bill. Though his record with GOP bills in times past suggest rather casts doubt on his chances of success...