To update, I ended up stopping the connection to my shop because it zero'ed out my inventory and I lost sales. I had already let it run for 4 hours and it was only at 7500 skus (I have over 400 listings each with 70 variations so about 28k skus total by Shipstation math. Those 70 variations are the same for each listing so realistically only 70 skus.) After 4 hours, it wasn't even half way completed which means it would have taken days to fully sync. I made sales at the start of the sync, prior to it somehow changing my stock to zero which obviously didn't sync so the numbers were skewed almost immediately.
I'll stick with my current inventory app. While it may be a little quirky and the view is messy, it works. It has no problem syncing my numbers within minutes for two shops. It doesn't let me oversell and it certainly doesn't change my stock to sold out when it's updating. Shame on Shipstation for rolling out a product that is clearly not ready for use.
