This is more so an improvement for marketpress that needs to be fixed in the next version. I have managed the rectify the problem but as it stands this will be the scenario everytime I need to update Marketpress.
We have custom gateways for payment & shipping. Every time we upgrade, part of the upgrade process is to delete those folders and refresh them with defaults.
Each time it happens I have to manually upload my custom files to the respective folders every time I update.
The solution us users really need is for the folders to not delete custom files out of those folders. The folders it deletes are in side the plugin folder;
Our store is live and works great however this happened yesterday when we upgraded and we didn't find out until this morning so we missed out on 1 day worth of sales.