Reports not matching and Database Utilities tool not working

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I am having an issue with inventory reports not matching, and showing false negative quantities. The inventory quantity report will sometimes show negative Pending Sales Order quantities, and currently I am seeing negative quantities for some items only on the Inventory Summary report, but those items are showing as zero quantity everywhere else (item record, other reports, etc). Our system is set to not allow negative quantities. Adding back the negative quantity brings the Inventory Summary report to zero, but then shows positive quantity everywhere else. This is a recurring issue we have been having for years, and running the Database Utilities tool has always fixed it. I have been told in the past that editing a sales order after it has been partially filled is the cause of the issue, and unfortunately that is something we do all the time as we routinely have large customer orders that are fulfilled in batches and then the original sales order is edited to remove the fulfilled items and leave the rest as a back-order.

Since sometime last year, the Database Utility tool has stopped working, it just closes out without having fixed anything. I have also tried the Company File Check & Repair, which also does nothing. I spoke to a tech support agent last year, he was baffled that the tool wasn't doing anything, and instead ran some process that end users do not have access to which did fix the issue at the time. But as more sales orders have been altered since then, I now have more items showing false negative quantities.

I am wondering if there is anything I can do myself to fix this and avoid having to call tech support and walk through the entire issue every time I start seeing negative quantities?