I recommend you always use soft start when starting up your hot runner system. If you use filled resins or resins with short residence time, you should purge the system out one a week or each time you shut the system down. This will prevent your system from premature issues from wear. I would recommend you take the system apart and inspect it every 6 months minimum.
Soft start is designed to make sure any moisture that may get into the heaters will be baked out at low slow temperature rise before higher temperatures are applied. This will prevent your heaters burning out prematurely. Many times when I have to trouble shoot a hot runner in the field, a customer has issues starting up a system that has been running a filled resin. The suggestion of cleaning out the filed resin at shut down would not void a warranty. In fact, if the hot runner supplier heard that they would support it. As far as the timing of you doing general maintenance, it is recommended you follow the provided guide lines from the original hot runner supplier. If a system has been passed along to more than 1 molder, then these instructions are sometimes not passed along this would be a general suggestion.