Deleting Payment/Shipping Modules

Forgive the stupid newbie question....

I'm preparing to upgrade from 1.3.7 and am reading all the FAQs etc. I know that payment/shipping modules need to be deleted prior to upgrade and reinstalled afterwards. I just wanted to check exactly when that needs to be done, I'm assuming at the last minute?

The WinMerge comparing/changing of files stage is going to take a while as the site is highly customised - the live site will stay live during this process so the payment/shipping modules will need to be there? Or by not deleting them prior to doing the WinMerge stage, is it going to cause issues when comparing files?

Again sorry for the probably very stupid question, never done an upgrade before (or an install for that matter) and just want to make sure I know exactly what I'm doing.

Thank you!

You're talking as though you're intending to do an upgrade directly to your live site. DON'T.

Install a COPY of your live site onto your PC or into another folder+database on your server. Do the upgrade there FIRST. Work out all the kinks. Take good notes.
THEN when you're sure you've got it all ready, AND ONLY THEN, then you re-do the upgrade on the live site. That way the live site will only be down for a few minutes instead of possibly for several days while you sort out a quirk somewhere.
THAT is why the upgrade instructions are written the way they are.

DrByte:

You're talking as though you're intending to do an upgrade directly to your live site. DON'T.

Install a COPY of your live site onto your PC or into another folder+database on your server. Do the upgrade there FIRST. Work out all the kinks. Take good notes.
THEN when you're sure you've got it all ready, AND ONLY THEN, then you re-do the upgrade on the live site. That way the live site will only be down for a few minutes instead of possibly for several days while you sort out a quirk somewhere.
THAT is why the upgrade instructions are written the way they are.

Thank you very much for the reply, that makes sense.

There is no way I would upgrade the live site - I'm going to do a test site on the server, sorry I wasn't clear.

There are 2 parts involved in "deleting shipping/payment modules": The admin part, and the "files" part.

a) in your Admin, click the "Edit" button and record all the settings for the module. Repeat for each module.
b) click Remove to delete that module's settings from your store
c) now upgrade the files on your server (replace old files with new ones, delete files that need deleting, etc)
d) once the upgrade of files is done, go back into your admin and click Install on the modules you need for your store, and reconfigure them. For the most part you'll have the information you need written down.