Are there rules anywhere for reprogramming droids?
If you just want to reprogram a droid for different loyalties, or maybe a different personality, I would think that might just be an opposed roll of Computers vs, the droid's Discipline. And then you end up with a droid who likes the Rebellion instead of the Empire.
If you want to "reprogram" a droid so its skills are better (to improve its prime directives), that might be a Computers check with the difficulty based on what you're trying to accomplish. Say, improving the droid's existing Ranged (Light) skill by 1 might be an Average difficulty. Adding Tricky Target to a pilot droid's repertoire might be a Hard difficulty check.
Adding a second pair of arms would be a Mechanics check to assemble, and then a Computers check to add the software that would allow the droid make proper use of those arms (the Additional Limbs benefit some species have).
But how does one reprogram a droid to perform a different job altogether? Do you use the droid crafting rules in Special Modifications?
What I'm thinking...
Step 1: Select Template. In this case, no matter what the droid was previously programmed for, you are selecting its new template.
Step 2: Acquire Materials. You have an existing droid. It is already acquired. But, how you got the droid, and what shape it is in, can certainly vary. It can cost money; it can cost adventure. Whatever.
Step 3: Chassis Construction. "But, Rich. The droid is already built. Why am I making this roll?" The droid chassis may already be built, but it may need repairs or you might need to rebuild it some for its new programming. Turning a protocol droid into an assassin droid might require giving its arms more flexibility or attaching blades to its fingers. Recycling the remains of a couple deactivated battle droids into the crew's new co-pilot droid might require some significant repair work. If you already have a droid-person that you are reprogramming, make the Mechanics check one difficulty easier for the intended new chassis.
Step 4: Program Directives. Here is where you are replacing the droid's old programming with the new. The check stands as it is in Table 3-9, but upgrade the difficulty a number of times equal to the droid's Willpower (or Intellect maybe?) because you are trying to overwrite old coding that you might find undesirable but that the droid sees as its core self. Add one or more Setback Dice if the new programming is vastly different from the old.
For the droidcrafter, reprogramming a droid instead of building a new one offers a benefit but at a cost. Acquiring materials and building the chassis is easier, unless you really have something more specific in mind such as building a protocol droid out of an IG-100 that you have yet to acquire. But then programming the new directives is more difficult.