Shotcut rejects changes to master folder and playlist

I’m working on a video composed of a mix of stills and video clips – over 100 files.
My method has been: (1) put all files in one master folder, (2) number them sequentially, (3) open all in Shotcut (this automatically puts them in the Playlist), (4) add entire Playlist to timeline, (5) Export video.
So far, so good.
Now I have about a dozen items (files) that either should be repositioned or replaced with different files. So far the only way I’ve found to do this is to add/reposition items on the timeline.
This works, but it leaves me with a master folder that does not represent the current project, and a playlist that does not represent the current timeline. After a few changes it’s hard to keep track of what changes have been made.
I’ve tried making the changes in the master folder and also in the playlist, but Shotcut seems to remember the original version and rejects the changes (any file changed in this manner results in an ‘INVALID’ message when the video is played.
Question: Is there a way to make changes and also get the master folder, the playlist and the timeline all with the same contents in the same sequence? Without getting ‘INVALID’ frames?