Sorry to say but, you just messed up. There IS a limit on the amount of C-Bills your mercenary company can have after which it will "loop" to the debt. You will need to load an older savegame to fix it. Otherwise you'll have to start a new game.
You can't go over 2 Billion c-bills iirc, that's the threshold before it starts looping to negatives
I have currently tested the 99 items option and it worked perfectly fine. Follow the instructions below.
again, you have to BUY something first. option only works in the STORE. Click you main ship tab (LEAPORD or whatever), then click STORE, then click BUY, then BUY an item that is infinite supply and cheap (like SRM AMMO). Then toggle this option on and then buy an item that has a set number of them left, and it sets the item to 99. You will have to leave the STORE then come back to see it is now 99.
This does work and the stock go's back to 99 after you have bought them and went back in the store.
Video showing it using the feature -> Link