Normally the command updates automatically based on changes to the parm interface, but once you enable explicit editing of the FFMPEG command line that'll no longer be the case. There are two portions of the command that you'll need to keep intact to ensure that it works as expected -- the input file list and the output file path.
Input image files are specified using a frame list file, rather than directly listing the image files in the command. This is technically only required if the list of input images is longer than your platform's shell command length limit, however for consistency the frame list file is used in all cases. That file is specified as the input in the command line string using the following:
-i "$PDG_TEMP/$HIPNAME.$OS.`@pdg_index`_framelist.txt"
PDG writes the frame list file for you, so as long as you include that as your input to the ffmpeg executable it should find the images.
If you're using the "Convert" preset instead, e.g. to convert an existing file from .mp4 to .gif, then the input file is specified directly using an expression instead of a framelist file:
-i "`pdginput(0, file/video, 0)`"
The output movie file is the last argument in the command line:
"$HIP/video/$HIPNAME.$OS.`@pdg_index`.mp4"
Once you enable manual editing of the command, changes to other parms on the node will no longer affect the command line string. You'll need to manually add/remove flags as needed.