There has to be some cause of the sudden mini cycle. Can you think of any thing that might have caused it? (untreated chlorinated water, filters became clogged, turn off filter too long, dead fish, overfeeding, etc.)
You mentioned a substrate change, I am not sure if eco-complete causes any problems, but sometimes substrates trap wastes underneath (especially sand that compacts easily) it and when disturbed/removed it kicks it all back up all the sudden and can cause spikes (hence why I recommend changing substrate without fish in tank, among other thing). Also the substrate does house some beneficial bacteria so that is lost with a substrate change, but it is minimal and I don't believe the amount lost causes a noticeable mini cycle cloud (unless it was a undergravel filter, which shouldn't be since you had sand).
I think you will be fine as long as the new filter has enough established media. I've never used eco-complete, but I doubt it leaches ammonia or it wouldn't be a recommended substrate.