Custom PHP Script Installation/Bug Fix

We have four Magento stores and an existing program already custom written that syncs our POS system with our Magento inventory. The script's purpose is to import new products from our POS system and update their stock/prices via a cron job. It does this well but whenever we make changes in Magento itself to items (change category, etc.) they seem to be overwritten by the program when it updates. This is a bug we need fixed. Also, only two of these stores has the program installed, two of them do not. Our existing programmer's schedule has changed and he can't continue in the time frame we require to install it on the other stores or try to find the overwriting issue. It is written in PHP so any experienced PHP programmer with a little Magento knowledge can probably do this for us. As an aside, Magento has its own bug that won't allow us to export our large inventory (20k items) without using the shell so finding a fix or workaround for that would be a great bonus.