Not sure if this is intentional behaviour or not but I noticed that regardless of using fixtures or the “export customizations” button, any fields added through “customize form” or “edit doctype” are not exported. Therefore when you update you lose all of them.
The way around this is to add them through the “custom fields” doctype, which will allow you to export them via fixtures.
It would be helpful though to be able to export fields added via “customize form” or “edit doctype” as this is a much more intuitive way of changing forms. If I’m missing something and I just didn’t do it right, please let me know.