There's a bug where once you unlock a discount on purchase price on upgrades, the button for the upgrade will light up before it will actually give you a benefit. For example, the button may be enabled with (0, so adding +0. You can still click the button but you get nothing and pay the price anyway.
I was playing and my doubloons just mysteriously disappeared and the game reset as if I'd done a reset to get doubloons. I didn't lose upgrades nor gain an upgrade, I just went back to 0 on all numbers without clicking anything.
I'm sorry to hear that. I'm not sure yet what the problem could be, but I'll look into it. Also, if you PM me I can help you get them back.