For 3 years I never took the pump and filter in ---- Just drained and pulled the plugs and that was it ------ Last year I read a piece on Hayward's website saying that the pump should be stored inside because the area near the seal has a small chamber which can not be drained easily. That may explain why I had to replace the seal the spring after year 3. I installed a waterproof plug and socket on the pump's electrical and now bring it in every year.
Your question about breaking things apart at the unions ---- Unless you have a very tight configuration and things are small -- you probably will find it easier to take things apart. Unions tend to swivel anyhow so it will misalign everything anyhow.
Save yourself some aggravation and take it apart --- Also go to HD or Lowes and get a little container of plumbers silicon grease to lube the O-rings when you put things back together. It helps the seals in the valves also.
Good luck.
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