Apsona ShopAdmin - a free tool for import/mass update/reporting

[torvista]

I thought I could just update the number on my spreadsheet, import the csv file and create/update, but that seems to remove the file from the storefront,

Yes. It should update only the fields you are importing. If it is removing them, it must be either changing the enabled field to 0 or changing the category and/or master category.

A mass change is easy enough, but I if I have 50 different products in a category, and want to update them all to reflect their individual quanitity in stock,

I don't understand the distinction between these two cases.
An update of any product field is based on the id or unique model number, doesn't matter "where" they are.
Are you saying the group of products you want to update is just those in one particular category?

Second, is it possible to make a "Discount" or Special Pricing" column on a csv file to upload via Apsona

You have have any column you like in the spreadsheet. Apsona will not choke on it: it will just map the columns to field names it recognises, the others you can choose to map from the drop-down selector above the field, or not and they are ignored on the import.
I have an enormous spreadsheet for product control, most of which Apsona import can ignore with no problem.

If you can't map to where you want, contact Apsona, I think they can customise the code you download for you only.