No, no, no!!! Don't mess with your saddles with only some of the strings on the guitar!!!
You have to put ALL of the strings on a Strat before you can be sure there's a problem with it.
Taking off all the strings at once causes the trem block to drop back because the only tension on it is the springs. Having all of your strings on creates the balance between the string tension and the spring tension.
With any guitar, but ESPECIALLY with Strats or other trem guitars, when you change your strings (which you should do more than once every 6 months if you play it regularly!), change one at a time.
I.E., remove the low E and then replace it, tuning it to pitch. Next remove the low A an replace it, tuning it to pitch. Complete the process for each string.* FINISH THE PROCESS... then check final tuning, etc.
Now... you said you removed a spring, so that will require some tweaking once all the strings are on (including intonation being a good idea), but you can't even begin to tweak anything until all your strings are on the guitar and at pitch. This is probably why this is happening to you and never did before during string changes. I generally suggest adding/removing springs with the strings still on--unless you already have your trem set flush to the deck, you have to hold the trem up with the "whammy bar" and that's a little tricky while trying to add or remove the spring at the same time, but it allows you to RETUNE, then make the necessary adjustments to the claw while constantly checking and retuning to pitch, so you can again achieve the trem block position/balance you like.
Again, you'd always want to intonate after a spring add/remove, and some saddle adjustment (or sometimes neck adjustment/shim) might be needed, but either way you can't decide any of those things with a partially strung guitar.
Try to put your saddle(s) back where they were and get all the strings on there at pitch, then check it out and let us know. Good luck!!!
(* Note--I actually change them in this order: D, G, A, B, Low E, High E--inside working out, but that doesn't matter as much as being sure you do one at a time, at least on a Strat-type guitar)