Which pick will be lost?

Lots of twitter conversation and confusion over which pick the Astros would lose if they signed a free agent, like Choo or Ellsbury. Its clear the number 1 pick is safe, but there is a question whether they will lose the the competitive balance pick from the Orioles or the first pick in the 2nd round. Where those picks will fall, number wise, is yet to be determined, as the compensation pick for losing a FA will slot ahead of both picks.

The relevant text of the CBA is as follows.

i. A Club that signs one Qualified Free Agent who is subject
to compensation shall forfeit its highest available selection in the
next Rule 4 Draft. A Club that signs more than one Qualified Free
Agent subject to compensation shall forfeit its highest remaining
selection in the next Rule 4 Draft for each additional Qualified
Free Agent it signs. Notwithstanding the above, a Club shall not
be required to forfeit a selection in the top ten of the first round
of the Rule 4 Draft, and its highest available selection shall be
deemed its first selection following the tenth selection of the first
round.

ii. A Club’s highest available selection in the next Rule 4
Draft shall be determined after accounting for any selections the
Club forfeited for exceeding its Signing Bonus Pool in the Rule
4 Draft. With the exception of draft selections awarded to a Club
pursuant to Major League Rule 4(c)(2), all of a Club’s draft selections
will be subject to forfeiture pursuant to subsection 4(c)(i)
above, including draft selections obtained through assignments,
draft selections obtained in the Competitive Balance Lotteries
and Forfeited Draft Pick Lotteries, and draft selections awarded
as compensation pursuant to subsection 4(b) above.

In other words, the team loses its first pick outside of the top 10, with only one exception. Major League Rule 4(c)(2) provides a supplemental pick for the failure to sign a draft pick in the previous years' draft, and that pick cannot be forfeited. Other than that, a team loses its very first pick outside of the top 10, however acquired. So, if the Astros sign a Qualified Free Agent, they would lose the competitive balance pick acquired from the Orioles, which will probably be in the mid to late 30's once the dust settles. I hope this clears that up for everyone..