Sorry, I misspoke saying "no limit." I meant that there is nothing different - no special limitation that applies to MFS (separate) returns. So a taxpayer who qualifies to take $7100 for family coverage on a Joint return can use that same limit if the taxpayer files separately.  Of course the other spouse could not claim any deduction (or exemption) on form 8889 for an HSA.

The reason I ask is that when I copied the joint return data and changed/removed items to make it a separate return, ProConnect cut the $7100 amount which was on the MFJ return by 1/2 to $3550.  I changed it back (override) and no errors appear, but wanted to ask if the community agrees that it's acceptable to do this.

I think the consensus is "yes."