@Duraflex 

You need to run the Condense Data utility to remove old data and create a new company file with a condensed one. The problem is you will need to fix the Negative Inventory issue beforehand.

Run the Inventory Valuation Detail (IVD) report and select Reports>Inventory>Inventory Valuation Detail.

Click the Dates drop-down and select All.
Find all occurrence's of negative amounts in the On Hand column.

Scroll through the report to an item that is showing a negative amount in the On Hand column.
If you can do so legitimately, adjust the dates of the bills and/or invoices so that the bill dates are before the invoice dates.

Repeat those seps for each item with a negative quantity in the On Hand column. It is not sufficient to adjust the current QOH to a positive value. You must eliminate each occurrence of negative QOH.

If you don't have time to fix them, you can purchase a 3rd party service to do so during weekend to lower your downtime.