The PO utility "PURGE OBSOLETE POs" will purge ALL POs regardless of status prior to the cutoff date that you provide. 

Please note that this utility will remove backordered POs (whose amounts contribute to the Purchases Clearing Report) however it will not make any sort of GL entry to balance the Purchases Clearing account, so you have to do that part yourself.

Definitely print the Purchases Clearing report (in the Period End menu) before purging because deleting anything on that report has Accounting implications. 

If you want to keep selected PO's from before the purge date, edit them to a more recent date before running the utility.

So since we are not using the modules how they should be and my clearing report has a value of  -$3,518,985.66, with 630 pages,  I would not edit all these PO's.  My next question is does the "PURGE OBSOLETE" utility take the Purchase Order option setup in consideration?  We have "years to retain..." set to 5 years, so when/if I run the PURGE I can override this setting ?

Years To Retain... is for transaction history not PO's.  Open POs are never purged automatically, and completed PO's are purged based on a Days to Retain... setting.

Try in a test company if you really want to see what happens.

Here is the big question. If your purchases clearing report has a value of -$3,518,985.66  what is the value in your Purchases Clearing GL account?  What you have posted tells me you are not using the Purchase Order module correctly. Most likely you are entering the invoices through AP instead of PO. 

Correct, some invoices are being posted through PO if there is a PO to match with the vendor invoice, if we create a PO outside of Sage we post it in AP.  Where is the "Purchases Clearing GL account" ?

The Purchases Clearing Account is listed in Product Line Maintenance.  With the PO module you'd typically process receipts in one of two ways:

All-in-one transaction: Receipt of Goods with invoice.  (If you don't enter a PO in advance you can still do this).  There is no Purchases Clearing impact because you are posting directly to Inventory and AP.

Two transactions:  Receipt of Goods separate from Receipt of Invoice.  Since one transaction affects Inventory and the other AP, the transition is handled by Purchases Clearing (invoiced and not received or received and not invoiced), with the values stored in the open PO.  You want to regularly balance the PC GL account(s) with the Purchases Clearing report.

We have 35 different "product lines" probably 30 GL clearing accounts assigned to those 35 lines.

Sort the report by Product Line to make reconciliation easier.

You should find a reseller that knows what they are doing.  That sounds like a real mess.