As far as I know, you cannot revise either trunked or conventional by updating from Radio Reference; it will only add another version of what you already have. The only way I know to remove a system is to manually remove it by right clicking on it, then choosing delete every line item.
I presume that Arc500 works similar to Win500. In the software, you can highlight the existing system, go to Edit and delete the old system and TGID's. And yes even conventional if it is updated. Then using the import function, import the newer system and TGID's. Then upload the new file to the scanner. It will erase the old system and replace it with the new one Just that simple. HTH, Larry