OK, so, first off… let me make sure I understand the issue? It’s that you made some further changes to the navbar partial – and those changes didn’t seem to mark all the pages as needing upload. Correct?
If so, then this is kind of a long story. But before I get to that… a simple workaround is just to type Cmd-Shift-M or choose Mark all Pages as Changed. This won’t re-upload everything on your site – it just makes sure that RapidWeaver will export each page and look for changes that need to be uploaded – like your NavBar partial.
OK, longer version…
The truth is that when RapidWeaver 6.x and 7.0 were out this feature worked great… if you made a change to a partial, then all of the pages that utilized that partial would notice and mark themselves as changed.
But RapidWeaver 7.1 introduced some radical changes to the RapidWeaver API. One of those was to delay loading of pages in your site until they are absolutely needed. Unfortunately there wasn’t much help given to to plugins like Stacks that relied on those pages being loaded for some features.
For most features I was able to come up with a workaround that allowed things to mostly get handled the same was as pre RW 7.1 – but there just wasn’t anything to do for this one. It required a radical re-architecture of partials to make that feature work again.
I’ve been working on that – and I’ll be honest – even years later, I still haven’t completely managed to work around that one. But it will at least be far better in Stacks 4. In all but the a few corner cases it should do the right thing again.
Unfortunately there just isn’t a way to bring those huge changes back to Stacks 3. I hate it when a “bug fix” is included only in a big update. But I swear I didn’t do it on purpose – it really was just a massive massive rebuilding of how these things work.