You can't modify a die more than once, but APT clearly intends for you to turn blanks to focus, and then focus to hits, right? How does this work?

You can modify dice as many times as you want. You just can't reroll dice more than once. For example, sensor jammer modifies a hit to a focus. You may then spend your token to change it from a focus to a hit.

Or if you have TL+F, you can spend the TL to reroll a blank, and have it come up as a focus. At this time you can spend your focus to change it to a hit.

You have steps while attacking that you take

Roll attack dice (initial attack)

Defender can modify your attack dice (IE sensor jammer, elusiveness)

Then you get to modify your attack dice (IE spend Target lock, focus, mercenary co-pilot, marskmanship, any missile dice changes)

Since it states that any time simultaneous events happen the active player gets to choose the order, you are free to modify the dice to your advantage.

Example.

I shoot with Kath and HLC at range 3 while marksmanship and a Mercenary Copilot is active.

Crit, Hit, Focus, Focus.

HLC says that you turn all crits to hits, marksman can make 1 focus a crit and rest hits, and Merc copilot can change 1 hit to a crit at range 3.

First step would be to turn your crit down into a hit due to HLC. You can then Turn your Focus into a Crit and 1 hit via marskman, and turn another hit into a Crit

Leaving your final attack at Crit, Crit, Hit, Hit