Was it Quicken Essentials that you mean by being a "bare bones" version? Answering this will help how we proceed.Also, are you currently using 2017? You mentioned upgrading, but I don't know if that is the current version you are using.
If I understand correctly, the years of paycheck splits will result in a huge cash balance in the account. Since the download of investment transactions will likely cover at most 90 days, you will need to create 1 large Buy transaction using that coverts the excess cash balance to shares (for each security). The price calculated will become the average cost basis for those shares.If you don't create the Buy transaction, Quicken will probably create a placeholder transaction to make the share balance reach what the brokerage thinks you have. But this placeholder will not "use up" the cash balance. That's when the value of the account would then show double. Once you create the Buy transaction and all the shares are accounted for, the placeholder should disappear. If not, you can delete it manually.Placeholder transactions are at the start of the register (usually), in light gray, and have the word "placeholder" in the memo.
It would be important to know what version of Quicken you were using to enter all these manual investment transactions.
