The Stock on hand report and Shopify's own inventory figures are both right, and they usually differ for one of the reasons below. Check them before you go hunting for a sync problem.
Why the numbers differ
Available is not the same as on hand. The report leads with Available, which is what you can still sell. Shopify's inventory reporting quotes what is on hand. The gap between them is stock committed to orders that have not shipped yet - it is on your shelf, but it is already sold. Use Columns to show the On hand column and you can read both figures side by side.
Active products are counted by default. Stock sitting on draft or archived products is left out unless you ask for it, because the question the report answers out of the box is what you can sell and what that is worth. Shopify counts those units. If you have a rack of samples or a season's products still in draft, that alone can be a few hundred units. Use the Status filter above the table to switch between Active, Draft, Archived and All statuses - the rows, the totals and the CSV export all follow it.
One thing to know when you do switch it: the Stock value on the Inventory page always counts active products only. So on any setting other than Active, the value on this report is deliberately a different number, and the report says so underneath the table.
One more thing worth ruling out: locations you have hidden in Stockroom are excluded from stock reports entirely, and the All locations filter narrows the report to one location while Shopify's figure covers them all.
Good to know
Every report's filters, export and scheduling are in Reports in Stockroom.