Dear Allin,
I'm testing a bundle function which contains a scalar and a matrix. 
I saved the matrix normally. Then edited it and made some changes.
Eventually, I turn back to the bundle and wanted to save the original matrix with the same name (to replace the old one I modified). 
gretl prompts the warning "A matrix named...already exist. OK to overwrite?" and I choose "Yes". 
The result is that the old matrix is replicated instead of being replaced: same name, same content. If I repeat the operation several time the old matrix is replicated each time.
Besides, when selected "No" to the warning message and cancelled the saving process the old matrix is still replicated.