Not a single regex but one way to do what you want is to read your file in paragraph mode, with $/ and split the logic: 

{
  local $/ = ""; # Edit: added use of local for good practice

  while (<DATA>)
  {
    s/^##.*//s unless /^\w/m;
    print;
  }
}
__DATA__
## Remove

## Keep
this

## Remove

## Also keep
that

[download]

Otherwise you could use a negative look ahead assertion (?!^\w)

Edit: seems like I really didn't read the requirement well enough ^^"

In reply to Re: Tricky regex problem by Eily
in thread Tricky regex problem by nysus

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