Accepted to PhD program but declined, but now want to return 3 years later
I did something similar (2 years).  I just went ahead and reapplied.  5 of the 6 schools that accepted me previously did so over again.

Didn't even think about not doing the applications.  What's the big deal.  You should know how.  Let them run their process.

I recommend to apply to several schools.  Always good advice but in this case to hedge your bets in case "A" doesn't like how they were cold shouldered earlier.

I would try to put a positive spin on things but not dwell on the previous decline (no mea culpa).  'Have had 3 productive years doing X, but now see more than ever that my skills would better fit in a Ph.D. level position.'  Hopefully they still want you.  Of course for any schools that you didn't decline earlier, you don't need to mention it as much.  Just say you worked a while and decided you belong in Ph.D.