What is the best way to fix stock lots?

I think you  will need to start with the latest sell and reset the lots to no specific lots selected, then work your way back through the sells repeating the process until you get to the first sell that has the lot selection issue. Then work your way forward through the sells applying the correct lot selections. 

Not it a trivial effort. Be sure to back up before embarking on the clean up. 

saberman said:

Over a long period of time the stock lots in Quicken became different from the actual ones in my brokerage account. 

Is there a way to manually edit the stock lots?  I thought I could do it by editing the trades but that doesn't work because the correct lots are not available.

In what way are they different?
Why are they different?
What is the importance of this to you?  Taxes, cap gains estimates, your OCD nature (like mine), historical accuracy?

In addition to the suggestions by others, you could do a Remove Shares followed by Add Shares for each lot with the right (broker matched) basis and acquisition date for each lot.

A trick-of-the-trade would be to enter a Shares Transferred between Accounts transferring the security from the existing account to the same account.  That will generate the Remove Shares and a series of Add Shares based on Quicken's info about current lots.  You would then just need to edit, copy, or delete some of those Add Shares to correct the data.  That might be easier than individually creating the Add Shares transactions.  

Just keep in mind that such a Remove/Add sequence will not change history (in Quicken), so that may not meet your objective.