Sorry, but you can't show several separate workflows on one connected flow diagram. There rarely exists a general place from where control of mainloop is interrupted by external event (interrupt) -> thus the connection point between main and interrupt handler flow can't be described on flow diagram.
Only way is to draw several diagrams that show workflows of sequences which may run "in parallel" (RTOS processes) or blocking each other (Interrupts). Those sequences will have their start position marked by RESET, EXT_DATA_READY_EVENT or any other meaningful name describing the start of execution flow for this chart. Each sequence will have it's own end or even have no end marker.
These flow diagrams may share same flags/variables to show interdependency.
Sequence diagram may also be handy for you, but I suppose - it is not what you wanted primarily.