Did you load in Ajax? I've got a client that runs a site that loads HTML in separately. They've been paying for a third party service to run PhantomJS and save HTML snapshots to serve to Googlebot - is that no longer needed?
(I'm not thrilled about rendering this way, but it makes development a lot easier.)
In practice, and from experience... content changes driven by JS tend to lag a few days, if the content was changed via direct output... If you're doing client-side rendering, couldn't you refactor to use node, or similar for your output rendering?
If you aren't heavy reliant on conversions from search traffic, you can probably get away with being JS driven, I'd suggest sticking with Anchor tags for direct navigation with JS overrides. Assuming you are supporting full url changes.. otherwise you need to support he shebang alternate paths... which is/was a pain when I did it 3-4 years ago.
(I'm not thrilled about rendering this way, but it makes development a lot easier.)