I have a file with this at the top:

#+PROPERTY: header-args :tangle filename

And a lot of SRC blocks with this header:

#+BEGIN_SRC emacs-lisp
#+END_SRC

In the past, when I tangled the file, I got ~100 blocks exported. Now I get 5, because only 5 have explicit ":tangle" arguments in the header.

I just checked the NEWS file and did not see mention of this change. Has something changed with the header-arg properties? Babel?

It impossible to tell what's wrong with just that information. Can you share a minimum working example that demonstrates this? (something that should probably tangle 3 files but is instead tangling just 1?)

*** Old Babel header properties are no longer supported

Using header arguments as property names is no longer possible. As
such, the following

#+BEGIN_EXAMPLE
,* Headline
:PROPERTIES:
:exports: code
:var: a=1 b=2
:var+: c=3
:END:
#+END_EXAMPLE

should be written instead

#+BEGIN_EXAMPLE
,* Headline
:PROPERTIES:
:header-args: :exports code
:header-args+: :var a=1 b=2
:header-args+: :var c=3
:END:
#+END_EXAMPLE

Please note that, however, old properties were defined at the source
block definition. Current ones are defined where the block is called.