There are different ways to achieve it, but if you are disabling the middleman of mapped key of the rotation, rather than the steps, then anything that it calls that middleman mapped key wont run.
Other options
1. you can have a timer with a count of 1, set them to replace each time you set it. Setup all the skills that are in the rotation to use this timer, and the last one, sets 60 seconds. This way if you only get part way through it, the other spells cooldowns will be in effect for each step on the rotation, and as each gets actioned they force the timer to replace with a new setting. Note this breaks my prior rule of use individual timers for each step/action, but in this case you want them to be linked together. Sounds easy, but pretty sure it will stuff up easily.
2. Use virtualisation to swap sub rotations in and out. To do it, you may end up needing to have each sub rotation have a final step which will virtualise other rotations, but only if they are ready, so the other rotations actually need to manipulate a Control mapped key which is doing the virtualisation, and the final step of each rotation is to call that Control mapped key, and the Control mapped key will be stepping through it's virtualisation steps which is doing the swapping of the sub rotations.
Now 2 sounds tricky so I've made a paste of a config with a dummy setup. It is missing a few pieces of the sub rotations, with shutting down each rotation step and doing casttime cooldowns, but they may not be needed in this setup anyway. If they are, you should hopefully be able to fill them in from last time.
Just to explain it, the main setup uses virtualisation already, and this effectively is you mash on the 1 hotkey, and for the Tanker character, it will call the Do Rotations mapped key in the _999_ Tank keymap.
- Do Rotations calls Virtual Rotations. This has an implementation which actually calls Rotation Final. This is my low spec fallback, can always trigger this one skill. You might have an actual rotation set here too.
- The final step in the Rotation Final should call Control Rotations.
- Control Rotations runs it's first step, which virtualises the Virtual Rotations, and swaps it out for Rotation 1.
- Rotation 1 runs it's steps. Step 1 is a skill for the game, and also disables step 1 in Control Rotations. Step 2 is a skill for the game, and also sets a timer to re-enable Step 1 in Control Rotations for 60 secs. And it calls Control Rotations
- Control Rotations runs step 2 (step 1 is disabled as well), which virtualises the Virtual Rotations, and swaps it out for Rotation 2.
- Rotation 2 runs it's steps. Step 1 is a skill for the game, and also disables step 2 in Control Rotations. Step 2 is a skill for the game, and also sets a timer to re-enable Step 2 in Control Rotations for 30 secs. And it calls Control Rotations
- Control Rotations runs step 3 (step 2is disabled as well, potentionally step 1 is still disabled), which removes the virtualisation on Virtual Rotations, which goes back to what it is setup to do, and call Rotation Final.
- Rotation Final runs. This is my low spec fallback, can always trigger this one skill. You might have an actual rotation set here too. Step 1 sends a skill to the game, and calls Control Rotation.
- Now depending on whether the timers to re-enable Step 1 or Step 2 of Control Rotation have fired, it will pretty much just run step 3 here again (i.e. repeat 7 and 8) until Step 2 is renabled. When step 2 is renabled, then 5 and 6 will repeat, and depending on the timer for step 1, will either switch back to Rotation Final, or re-enable Rotation 1......
Now that is pretty cool.
The config that goes with it. This is a full config, so I suggest you open a second copy of ISBoxer Toolkit to view it. Copy all the text on this page, right click the ISBoxer node at the top of the toolkit, and select Paste ISBoxer Toolkit Profile from Clipboard.
http://pastebin.com/raw/rWVyDmwT/e: updated the paste as it was missing a couple of actions.... hah..