Ah....very timely topic as we just did the same thing just a bit north of you.
Very important to have clear coordination and communication between all involved or it can be a sh*t-show....;-)
When a "step cut" exists between the fairway and primary rough, there are two ways to remove it: "Lower the bridge or raise the river"...;-)
Meaning: 1) mow the step cut down to fairway height or 2) grow the step cut to rough height.
This assumes, however, that the grass types are the same and in many cases they are not. When we embraked on a restoration, we knew that an entire cut of grass would be eliminated from the course. In earnest and in haste last year, we thought we would be cute and remove step cut ASAP even before bunker work and tree work began.
So, we let our step cut grow out to height of the primary rough. Ouch, here's what ensued:
1. The fairways were effectively narrowed by ~8' (no big deal at our course)
2. The new rough, where old first cut was, came in thick and nasty and was cut at same level as primary rough or close to 2.5" (maybe 3"). It had also been fertilized.
3. Members would miss FW by 1' and have trouble finding their ball....;-)
4. Average round times spiked as this slowed play.
This year, now that restoration project has been completed (first stages at least), it is much better. Rough is mowed lower overall and balls that drift into primary cut can be played with just usual lack of spin, etc. It definitely saves maintenance and we also believe it looks cleaner. We also got rid of green fringes/collars and that has been received VERY well.
So, this trending practice, if done "right", can be very cool and will be received well. But, it sounds as if you are experiencing what we did last year.