Hi Boris,
Thanks for your post!
If you have run IV Reconcile and didn't see any change then we know your quantities are what the detail says they should be. I wouldn't expect running CheckLinks to help or be necessary in this instance.
I have some additional things for you to think about and look into however -
When you look at your Item Stock Inquiry at the very first line, do the amount "make sense?" Meaning if the Quantity In was was 10 for example, is the Balance also 10? If so, then we know all your detail records are there and correct. If that first line doesn't balance, then there is an issue in the detail somewhere. I would recommend reviewing the article titled:
The Balance in Item Stock Inquiry is incorrect in Microsoft Dynamics GP
https://support.microsoft.com/en-US/help/2647425
If you print the regular Stock Status report what do you see for quantities?
What about the Purchase Receipts report?
The thing with those 2 reports is that they are "real time" and give current quantity information. Since you mention that you do not allow your inventory to go negative, I am wondering if there is a timing difference (perhaps the transaction was backdated making it look like you were negative at the time when you really weren't?) that would be causing it to show like it does on the HSSR.
I hope you are able to find the smoking gun in one of these things. Good luck!
Pam
Microsoft Dynamics GP Support