Well , when multicam has "lost" some camera(s) , it pop ups a blank popup window with nothing on it.When i see this popup i know that a camera has lost connection.From this point no command can be issued so i have to reconnect them.
Did I mention you should try not using the GUI?

The blank popup means there was an unhandled error somewhere. Unfortunately IUP default error handling doesn't play nicely throwing non-string errors, while chdkptp throws an "error object" table to provide finer grained error handling.
Most of the stock chkdptp code should catch any errors and give you a proper stack trace, but it's possible I've missed some places. If you are using custom GUI code that's just calling multicam functions from a button callback or something like that, it would also have this problem. Since you haven't published the code, I can't give you much help with that.
In general, if you have a callback that calls chdkptp functions, you can do something like
mybutton.action=errutil.warp(function()...end)
where the inner function is whatever your normal callback would be. That will cause errors to go to the console.
Another "message" i see with "delete" command is (i will try to describe it since i don't quite remember it)..it displays in the console the actual command that is used and below that something like <id> : I/O error.
IO error means that some problem has happened with the USB connection. So this is probably due to your general USB stability problems, and not specific to delete.
PS : at some point of the tests... i had an error/message ...something like "cannot send <name of command> command : msg queue full. From that point nothing was working..i had to reboot ALL cameras.Any ideas about that?
That should mean that the one (or more) of the cameras was not processing messages as fast as you were sending them. Without knowing more about the specific sequence of events, I would be very difficult for me to guess what is happening.
multicam commands are implemented as messages sent with chdkptp <connection>:write_msg. The camera side script (rlib code at the bottom of multicam.lua) sits in loop waiting for messages. The message system has a queue that can hold up to 15 messages. Normally, you should wait for the previous command to be processed before attempting a new one, by using cmdwait or a hard coded delay.