When merging or deleting pages I would like to be able to overwright one of the files so that the file name and location is preserved.  This is to avoid errors in filenaming.  Any suggestions?

I did think about it, not only for deleting but also for inserting, extracting, rotating and security.

I think both methods have pros and cons, so the best way should be to insert an option in a configuration page to let the user choose the one he prefers. I will insert it in the next version (don't know when I'm going to do it).

For the "merging" function I think it is better as it works now.