Can a voltage stepper work on "negative" voltage?
Since I want to be able to use the same torquer to turn in both direction I'm using a H-bridge (l293d) in order to reverse the voltage.


That's a horribly antiquated part, and as explained just about every one of the numerous times it has been mentioned on this site, the use of Darlington transistors in it means that there is a very high voltage drop in both the high side and low side switches.  For ordinary purposes you should probably use a modern MOSFET based bridge, especially for low voltage applications.   These are now available in things like QFN packages which are much smaller and heatsink well to the board via a thermal pad.  The L293's DIP package would be particularly bad in a setting without convective air cooling.


  Now for my question, as the title says, will a step-up converter (Pololu u3v12f12) be able to step up a "negative" voltage?


No.  In theory it would be possible to build a converter which could accept input of either polarity and reflect that on the output but it would be absurdly complicated, and utterly unjustified.

What you should be doing is applying any needed voltage boost before the H-Bridge


  I didn't mix the order because I don't want to burn the h-bridge I wanted to step up it's output instead of giving it higher input


You obviously haven't read the L293 data sheet.  It has far more voltage handling capability in its ratings than it has current capability.  

No matter what you do with it, the thermal dissipation of the package will still be a potential limitation given the horribly lossy design - but operating it in an higher voltage lower current regime will get more from it than operating it in a lower voltage higher current one.

You need to pick an FET bridge matched to the voltage and current requirements of your motor.  If you are going to also employ a step up voltage booster, that goes before the H-bridge, and will have to be selected with the behavior of the load in mind - for example, don't forget to consider that if the transducer can be mechanically rotated, it may inject power back through the H-bridge circuit and diodes to the power supply, something not all such implementations can tolerate.

It also sounds like all of this needs to be space qualified, which brings in many other concerns.   Hopefully what you are building is a sort of mock-up... if this is actually going to fly, you need expert advice from someone who is not only orders of magnitude more aware of engineering issues in general, but with spaceflight issues specifically.  If in their opinion unique concerns of the spaceflight environment make a bipolar solution preferable to a MOS one, they will be able to guide you in selecting a suitable solution - not only for the bridge, but also for the voltage booster as pretty much all of the common everyday solutions to that you might by from a hobby vendor like Pololu are also MOSFET based.