Yes, I'll submit an update to Autodesk that makes disabling the link permanent this week. It typically takes them a few days to review and approve.
Some background:
Yes, Ripple keeps 1 space linked to 1 zone. I wrote a little about HVAC Zones here: https://rippleengineeringsoftware.com/running-hvac-heating-and-cooling-loads-in-revit/. The pertinent part is copied below. Essentially, my suggestion is to not use the Revit “HVAC Zones”. Instead, you can use the “Ripple-AHU Zone” and the “Ripple-VAV Zone” to indicate zoning. This has the added benefit of being automatically assigned using the AutoZoning tool. Here’s a demonstration of how the VAV Zoning works. https://youtu.be/_t2e-gC8-Po?t=890
You can disable the Zones to Spaces Link under the help menu (see image below). But I recommend not using HVAC Zones and instead use the “Ripple-AHU Zone” and “Ripple-VAV Zone” Parameters for the following reasons:
1) They can be automatically assigned using the “Auto Zoning” Tool
2) This way you can feed data from your zones to automatic equipment selections (VAV AutoSelect and a soon to be released AHU AutoSelect).
3) You can still make color-coded zoning charts like below with color schemes.
4) HVAC Zones only allow one zone type, when you will need at least 2. (AHU/ventilation and Terminal Unit/Thermal).


Revit HVAC Zones: The HVAC Zones category in Revit has some issues. There’s no clear direction on what the HVAC Zone is supposed to be. Is it a terminal unit zone? An AHU zone? A ventilation zone? The HVAC Zones contain data behavior that would apply to all of these zone types. For instance, when calculating loads, any space on that zone that is marked plenum (yes/no “Plenum” Parameter is checked) will not have a load calculated and reported. Instead, it will attempt to apply that load to the return air of the AHU (or whatever system type you have selected). This sounds okay in theory, but the HVAC Zone also contains the temperature setpoints, so unless your whole AHU zone is going have the same temperature setpoint, you can’t use it as an AHU zone. For this reason, we need to totally disregard zones, when you see zones in the loads report, disregard them and look at spaces only. The Ripple HVAC Loads Toolkit will automatically keep 1 zone synced with 1 space and keep the space temperature setpoints synced, because the internal loads engine uses the zone temperature. This will happen in the background, so disregard zones. If you have been using HVAC Zones with Color Fill Legends for visualization, we suggest creating a different Space text parameter such as “AHU Zone” or “Terminal Unit Zone” which can accomplish the same task and be more descriptive of what you are trying to visualize.