Here is what Amazon says about Global SKUs:
A Global SKU uses a shared inventory pool between the United States, Canada, and/or Mexico. You can create a Global SKU by selecting "Existing Offer" when you go to create an offer in Seller Central. When using a Global SKU, the total amount of inventory applies to all marketplaces. For example, if you have 100 units of inventory, it will display that there are 100 units in United States, 100 units in Canada, and 100 units in Mexico. The 100 applies to all three countries and DOES NOT add up to a total of 300 units. If an item sells in Canada, then all marketplaces would show 99 units available.
This explains why stock sync to one marketplace was overwriting available stock on other marketplaces.
If this behavior is not desired, make sure to use "Marketplace-specific SKU" instead of "Global SKU"
Here is where more information could be found on this.