I recently cleared some uploaded portraits that I had no need of any longer ( not in use ) for those that would be in use. It would not allow me to replace the deleted files with new ones . It let me upload them but when I went to assign portrait they were not in the uploaded files. Is anyone else having this issue ?

So...more questions.

Was the old portrait in use by a character that was deleted or otherwise removed? If it had belonged to an existing character, had it been removed from use (by clearing it from the portrait selection screen) before the file was replaced? Was this on a player character, or a GM character?

I just went and tested, and everything seems to be working right on my end, but it was only limited testing with my GM character. I can try to break it more by using PCs and NPCs in addition to my GM character, if necessary.

I uploaded an image, selected it as a portrait, then removed it from use, and then deleted the image from the portraits, uploaded a new portrait in that slot, and was successfully able to choose the new upload as a portrait again.

In the case where I did NOT remove the portrait from being used before deleting the file and replacing it with a new file, the portrait automatically switched from old to new when the files were swapped on the portrait management page.

The characters were already removed from the game. The portrait remained. I went and removed them. That went to upload the new characters, and the image didn't show up. Its weird.

Did you try a forced refresh?  Sometimes things get stuck, and need a little kick to get them moving (sometimes happens with maps, for example).

So...

I have successfully deleted an NPC without their portrait being removed, then deleted the portrait, uploaded a new portrait in that slot, and selected that portrait with a new NPC.

I have removed a portrait from an NPC, uploaded a new portrait in that slot, and successfully selected that portrait with a new NPC.

I put an uploaded portrait on a PC, then moved them to hidden without changing the portrait, THEN deleted the portrait, and successfully uploaded a new portrait in the same slot for selection for use by another PC.

The only thing I haven't tried - because I'm not willing to dink around with other players' characters - is altering portraits on PCs that belong to PCs that don't have GM access. I can't break it with anything I've tried, NPC or PC, removing or not removing the portraits before replacing them, but the only characters I've attempted to manipulate have been characters that belong to players with GM access.

...just to ask the dumb question, silverelf, but you definitely checked the 'delete' box under the image, and then hit the 'Upload Portraits' button to remove it, and then went back in to 'Choose file' for the new image, and then hit 'Upload Portraits' again, right?

Yep. I am experimenting with it at the moment. XD

Here is what I have uploaded.

https://i.imgur.com/uPmZxqB.png

and what I see
https://i.imgur.com/mcnA1iU.png