The filter drawboxhas timeline editing support. You can see which filters support timeline editing:
$ ffmpeg -filters
…
Filters:
T. = Timeline support
.S = Slice threading
A = Audio input/output
V = Video input/output
N = Dynamic number and/or type of input/output
| = Source or sink filter
…
.. deshake V->V Stabilize shaky video.
T. drawbox V->V Draw a colored box on the input video.
T. drawgrid V->V Draw a colored grid on the input video.
You can see that drawboxthey drawgridhave timeline support, but deshakecurrently does not.
. 28-32, 60 . . .
ffmpeg -i small.ts -vf "drawbox=enable='between(n,28,32)' : x=10 : y=10 : w=50 \
: h=50 : color=red,drawbox=enable='gte(t,60)' : x=100 : y=100 : w=200 : \
h=200 : color=green" -codec:a copy small_with_box.ts