If I´m not mistaken thats the standard method.... and shown in the datasheet.
This is alo a standard situation. The programmer has it´s supply and the application has it´s supply.
Nothing different to a PC and a printer (both mains powered) have individual supplies...and datalines between them.
What to take care of:
* Avoid to connect both supplies
* (early) connect both GNDs
* expect ESD when connecting. --> Protect your signal lines.
* Don´t force a HIGH signal to an unpowered device (wihtout beeing sure the device can withstand this). Often the valid input voltage range is: "GND - 0.6V" --- to "VCC + 0.6V". This means: if power is down, then VCC = 0V and thus the upper limit is +0.6V for applying external signals.
I recommend to add the diagram with all informations, because it´s hard to combne all informatons form differnt posts and text and diagrams. This leads to misunderstanding of the whole problem.
Klaus