I changed the file extension of music files that are registered in the Collection. Will this change be applied to the Collection?

No, for the change to be applied to the Collection, the music files need to be reimported to the Collection after the file extension is changed.
*Because the waveform, time, CUE point, etc. data change when the file extension is modified, data from before this modification cannot be used as is.

Relocate and Auto Relocate also cannot be used when the music files are listed as Missing Files.