Update Question

I got a call from a client who was running a site, that I wasn’t managing for him, asking for my help with update. Here’s what I found.
1. Running WP 3.5.1
2. D/B was 900 mb
3. 15 plug in updates required.

I rolled the dice and updated the plug-ins without any issue.
However, apparently PHP My Admin can’t handle a d/b this size so I couldn’t do a cpnal or data based back up via PHP My Admin.

I was able to get a WP files copied over but don’t have a d/b back up except via an SQL backup via HeidiSQL.

So I’m wondering if anyone has any advice at this point.
What I was planning on deactivating all the existing plugins and update from 3.5.1 to 4.6.1 and then bringing up the plug-ins one at a time.

Can anyone provide advice?
Thanks

Dan