Hi, OK you've worried about gases from my old substrate.
I had this happen on one occasion - completely unexpected as substrate did not appear compacted & there was lots of root growth through the substrate (valisneria, swords, crypts etc) - water was only slightly cloudy as I'd removed few plants, was sorting them in a bin, glanced back at tank to see fish in distress, I lost everything live in the tank
Since that (unlikely) experience, I only do minor changes in my tanks with livestock present
I generally perform large weekly water changes so there's little drift between my tank vs tap water parameters
(tap water is very soft, ~ pH 6.4)
When planning a rescape, I just increase water changes so I don't need to worry about saving any "old" water
Day of, I begin with a 50% water change in tank, then drain water into whatever bin, add some (sinking) wood so fish will have some hiding areas, float plant trimmings on top of water (again for fish comfort), quickly net fish over etc
Fish will usually be fine with just an airstone or (gentle current) water pump for 24hours
I use 5x dose of Seachem Prime as it binds ammonia, nitrites, even nitrates (going back to initial studies on this product); Seachem Stability is also effective
If you're able to place an internal filter etc, fish can easily manage some days BUT do not feed
Unless you have incompatible fish, bagging is to be avoided as it is far more stressful to fish than being able to swim about a dim area with light current for water oxygenation
Check the integrity of the transport box - I assume you mean the Styro boxes that fish are commonly shipped in - as long as it's water secure, you can just use this for the "bin"
It's not my preference as it's very "white" & can be difficult to clean before use, but I've seen fish wholesalers use these as temporary tanks
With fish safely & reasonably low stress "stored", you can relax while changing over the tank, take more time over hardscape & planting, change out clouded water or wait for it to clear before adding fish etc
Note if you do bag fish, do not feed for at least 24 hours, 48 is better!
if I was to sieve and just keep the ball soil from the old and completely change the bottom layer with a fresh batch of the jbl aqua soil would that be better?
I don't have a clear idea of what the "ball soil" might be, you may find that as you attempt to wash or sieve, it just "muds"
If this happens, definitely dispose
Washing soil can be a frustrating & time consuming process, consider if it's worth the budget savings
If you do want to retain the old substrate, I'd definitely set fish up in a suitable bin - without the time pressure you can enjoy the process
😀