Thanks for the detailed report, this is really useful.
The good news is those upgrades are not actually broken. Your Coilworks Scrap/Wave has been paying out every wave the whole time. The problem was the Scrap/Wave row in the battle screen showing the wrong number. It was only counting the small per-run part of the upgrade, which resets to 0 at the start of every run, and ignoring your permanent Coilworks investment. So it read 0 even while you were earning the scrap. That is fixed now, and the row will show the real total you earn each wave.
As for the others: Charge/Wave was working too, it just did not have its own row in the battle screen, so nothing on screen told you it was active. I am adding a row for it so it shows up the same way Scrap/Wave does. Charge Bonus and Scrap per Kill work a little differently. They are passive boosts that multiply your charge and your kill scrap automatically in the background, so they do not get their own row, but they are definitely on once you buy them.
Short version: you did not lose anything, you were getting all the bonuses, the screen just was not showing them. Thanks again for taking the time to write it up, it helped me pin down exactly what to fix.