Where I believe to have gone wrong is using old substrate that had not been stored properly. The substrate is a mix of eco-complete and pool filter sand. It sat outside in open topped five gallon buckets for two years.
Eco complete is a nutrient supplying substrate that helps compensate for the fact that most fertilizer don't have all the nutrients plants need. So if your water doesn't have a particular nutrient and the fertilizer doesn't have enough the substrate can supply it.
however the substrate doesn't have an infinite supply of mineral in it. So eventually it will run out of nutrients. By storing it outside for 2 years rain water filled and overflowed the bucket many times washing some nutrients away. The cleaning you did before putting it back in the aquarium may have depleted it even more. Although it may still look like new it may be severely depleted.
Eco-complete can be used endlessly if stored and used properly. It will absorb any added liquid fertilizer and remain vital.
If the fertilizer and tap water has the nutrient then yes it can store some. But if it doesn't the substrate will eventually run out. The places where the plants have died have probably run out of nutrients.The remaining healthy plants may be on good substrate and able to keep going. The pool filter sand you added is inert and probably has some limited ability to store some nutrients. But not enough to make a difference.
I have med-high light (Fluval 3.0 + Finnex 24/7 Planted+), CO2 injection and dosing full line of seachem ferts as per their chart.
Flourish Comprehensive is one of the products on the chart. It alone has all but one of the nutrients plants need listed on the bottle. So why are another 7 Seachem products on the chart? Simple the other 7 products are needed to compensate for the poor nutrient balance in comphrehansive.
For Example calcium and magnesium are macro nutrients plants need. Comprehensive only supplies these to parts per billion levels. Plants need them at parts per million level. So Seachem added Equilibrium to the list. Comprehensive is also week on nitrogen and phosphate so those two produce were also added to the chart. The type of iron used in comprehensive doesn't last long so additional bottle of iron was added to the list. Copper and zinc are only available in comprehensive a parts per trillion levels so a Seach trace as added to thee list.
Most of the products on the list are patches to correct problems in Seachems most popular product, Flourish Comprehensive.
Overall the easiest thing you could do to help your tank is to replace the old eco complete with new material. But overall you probably should think about trying a different fertilizer. Nilocg Thrive is worth considering It still is missing some nutrients but Tap water typically has enough. Others on this forum buy N,P,K and CSM+B (for micros) Many have good success with that but even that isn't perfect. Now some people on this site now making there own micros and macro fertilzers.