I noticed something interesting with regard to this glitch in my game today. For the most part, the plant revert glitch seemed to largely improve for me with the garden patches/fixes that came after the pre-Eco Lifestyle patch. After the purported fixes, occasionally a couple of the plants in my Sim's large garden would still revert to dirt piles, but the majority of the garden would be fine. However, today I added the great soil lot trait & the first day at 7 a.m. after the addition of that trait, almost all of the plants in my Sim's garden once again reverted to dirt piles. I quit without saving & reloaded the save a few times from around 3 a.m. & noticed that if I was on speed 1 when 7 a.m. rolled around again, almost all of the plants reverted to dirt piles, but on speed 2 or 3 at 7 a.m., the garden would be fine. Then, I tried saving my game at around 6:40 a.m. before reloading. This time, I noticed that on speed 1 at 7 a.m., the plants would briefly flash/glitch but they stayed harvestable & at speed 2 or 3 the plants were fine with no noticeable flash/glitch at 7 a.m. I don't know if this data point is helpful to anyone, but I thought I would post it just in case someone might find it useful. Needless to say, I'm going to remove the great soil trait & see if gardening for my Sim goes back to a mostly glitch free experience again.
Edited to add that when I removed the great soil trait, the notable plant flash/glitch at 7 a.m. on speed 1 was gone. So, while I don't think the trait is the sole cause for the revert glitch, I suspect that it is broken.