I am not sure what sql scripts you have issued against your hq db, or any triggers that might be in place, but let's say that the scripts were not harmful and not triggers are in place - It is possible that if you have different tax structures at stores from HQ, you would see this conflict on the SO side where updated tax would not list, and errors would be received on the HQ worksheet as well as you will receive an error on the store side relating to 'duplicate tax entry'.
Did you receive any errors, have an example of your tax structure on a manufacturer, RMS version #?
I do not know if this is at all related to your issue - but this is something that has happened to us with taxes:
This is all based on huge assumptions (I know) on something I have seen before. HQ has one generic tax structure that does not encompass any tax authorities. Many stores were built out to this same generic tax structure. Because tax was not centrally owned at the HQ level, stores had the ability to change and modify - which would work if you do not need a tax authority structure. Our stores required this structure, or did not like the wording if the generic 'Sales Tax', changing it to their state code + State Tax (i.e. MN State Tax). What these store level mods brought with them was a duplicate record issuing and conflict. The HQ tax code and SO tax codes remained the same, while the descriptions had been modified. All taxes were stripped out. The store had to delete the duplicated line item of Sales Tax and run a Task
190: Assign Item Sales Tax. Because of these issues, our stores are now required to run the Wizard on a monthly basis, or more often if needed, as HQ is now releasing items w/out tax assigned.