That was definitely a kitting error by Oscar (earlier kits) or CEDS (later kits) as both
encoders should be the same, just like all LEDs should be the same size, shade of
red, and brightness.
What likely happened is that Oscar / CEDS said "send me 500 more" to the same
supplier they had been using, got a bag with the same part number as before, and
put them in the bin with the few remaining older parts.
If you're comfortable with de-soldering one of the rotary switches, send pictures of
both to CEDS and ask for a replacement that matches one of yours. Then de-solder
the different one and install the replacement.
While there is support for both old-style and new-style encoders in my fork (which
will eventually become the official version), mismatched encoders is not something
that happens often enough (I think yours is the second or third case I've heard of in
6500+ shipped kits) to support.