I'd say: working but a bit unstable. I just installed El Capitan 10.11.1. Quicken 2007 for Lion seemed fine for a while, but then the toolbar disappeared. I tried adding a tab to the toolbar, and all the windows disappeared. Then Quicken crashed. I fixed the problem by quitting Quicken, restarting Quicken, letting it regenerate the dictionary and indexes, and checking the 'Show tabs' in the Configure Toolbar dialog box.
I suspect this will happen again in the future. This never happened for me under Mavericks or earlier OS's (I never used Yosemite).
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I also cannot comment about using any online tools. Which Quicken Version of 2007 Mac are you using 16.2.2 or 16.2.3? Or an earlier one? I upgraded to 16.2.3 under Yosemite and watched it for about a week. Everything worked great, unlike some Quicken 2007 upgrades in past. Then I upgraded OS to El Capitan and incredibly have had no Quicken problems.
Just seems a little faster, and (knock on wood) I have had none of the disappearing toolbar problems that I had with 16.2.2 under Yosemite. I was careful to rebuild files before each conversion, Quicken and Mac OS.
(the Command Option B thingy). I hope your miseries cease soon. BTW I'd be a little surprised if Q2007 16.2.1 would work with El Capitan.