How to Handle Investing Problem

I have been a Quicken user for many years. My investment portfolio has become out of control with respect to Quicken. Can seem to be able to reconcile without making a bigger mess of it. I feel like I should start over but am concerned about losing the links between my checking and the investments etc. Any guidance is appreciated.
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Answers
Are you concerned about accurate tracking of your cost basis and thus capital gains in Quicken?
Are you concerned about accurate tracking of your investment performance in Quicken?
If the answer to the last 2 questions is No and you only care about the account balances, the solution will be simpler.
What version of Quicken are you currently running?
If you do this Quicken will no longer have an accurate picture of your tax lots and cost basis, but you say your accounts are already messed up, so perhaps this is not an issue for you.
Also if you have not done so already, go to Edit > Preferences > Investment transactions and make sure "Show hidden transactions" is checked. This will make any Placeholders in your accounts visible. If you want to clean up the accounts, resolving the Placeholders will be an important first step.
Apparently there is a bug that causes the Update Cash balance dialog to appear when you use it with older data files.