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I can only recommend using herbicides and possibly a high water level(50+) combats them as well. I hardly ever need to weed anymore. The night material of the 5th "zone" of the island, Metallic sand, is a potent herbicide with no downsides. There's also salt but you need spring water or renowned water or the 1st zone night material, moonlit stone, to effectively counter the downside of that. The night material of the 3rd zone, aquatic drop, is a generally effective fertilizer additive that buffs all 4 of the stats a little bit. You can also try sending your friends out to gather at places with remedies. Reducing remedies, which are the herbicide one, can be found at the stream gathering area, just northwest of your home. If you send everyone there in the morning, you should get a couple by the end of the day.
Salt damage is a bit weird, I added fertilizer every morning with everything capped out and balanced the pesticides and immunites to be maxed out too, along with -100 Toxicity. And still the Salt damage kept crawling up throughout the year. It wasn't until I stopped using Salt entirely in fertilizer that it finally started going down, but very end of year it still kept crawling (and I still made sure to have -100 Toxicity every morning).
I want to say it's just about using Salt at all that causes it and trying to balance it out does nothing?
I did some basic testing after finding my new seedlings have about 20% salt damage after fully salt sorting. Basically, I would spread fertilizer with various components, plant the seedlings which would cause time to jump forward several hours, and observe what would reduce the salt damage. Also did two full cycles of rice just resting repeatedly and sometimes applying fertilizer that contained herbicides (metal sand), pesticides (fire stones) and remedies. At the start of the first cycle I dumped in 30ish salt and countered the toxicity and putting in one reducing remedy and I left the rice in high water the entire time. The second cycle was the same as the first but without dumping any salt into it. Some interesting things came up.
Dumping moonlit stones (or anything else that reduces toxicity) in your fertilizer is apparently a bad idea. With -100 toxicity, the salt damage stayed the same. However, what surprised me was my rice gained about 90% overgrown and spindly.
Second, just one reducing remedy eliminated the salt damage. This is a little surprising since reducing remedy increases herbicide but maybe makes sense in hindsight since it would reduce the excess salt. This lends support to an idea I had before that the various remedies are more effective than their values imply. Possibly they are unique in their ability to remove disorders through fertilizer.
Despite reducing remedies removing salt damage and increasing the herbicide rating, increasing the herbicide rating through other methods (mainly metal sand) would not affect the salt damage at all. This further supports the remedies being unique in their function. Not that it would make sense if herbicide rating itself removed salt damage since salt boosts that rating.
During the full cycle of rice, applying herbicides noticeably curbed or eliminated the weeds appearing in the patty. Similarly, pesticides would devastate the bug population.
Pecky rice disease, which is caused by excess insects (in this case swift larvae) can not be removed by remedies, except maybe reducing remedy which I ran out of by this time. You can stop it from increasing by applying pesticide though, which in turn kills the pests so it doesn't increase later.
In the first cycle, the salt damage rating would continuously reappear despite repeated applications of reducing remedy. One remedy at a time was enough to reduce it back to zero however. In the second cycle, the salt damage did not reappear after applying the first remedy except at the very end when the rice was ready to harvest but that was likely because I threw in a bunch of salt along with some remedies and other stuff to bring every status, pest, and weed to 0.
Immunity probably prevents your rice from catching diseases transmitted from insects or weeds. Herbicide kills weeds except seemingly algae or maybe the high water was just too good of an environment to be countered by high herbcide. Pesticide kills all insects and snails but frogs seem to be ok with it or might be the same situation as the algae.
Rice does not gain much, if any, stats during the night, but herbicides, pesticides, immunity, and remedies do work at night. Due to the limited slots of fertilizer, it may be a good idea to stack stat growth items regardless of the negative effects and apply it during the day and then counter this with fertilizer designed to heal your rice during the night.
As a side note, the aesthetic of my rice was shooting through the roof during this, with a high of 272 in one day during the second cycle. If I had the guess, the stats of the fertilizer are % bonuses rather than flat bonuses to the growth of your rice. During the first cycle I did not use stat boosters in my fertilizer at all and was still getting around 150 aesthetic. During the second cycle, I tried to use one medicine base and one cloudy crystal plus whatever powders and flakes I happened to have each day. This would mean strong fertilizer is not a replacement for growing your rice correctly for the stat you want to boost.
TL;DR herbicide wrecks weeds. Remedies can remove all rice disorders; for salt damage specifically, use reducing remedy. Salt damage will come back though if you use too much. Keep toxicity as close to 0 as possible, don't go below.
So you can remove this disease without using remedies? Nice :).
From my experience, sorting with mud is exactly what causes bakanae disease and probably rice blight as well. Sorting with salt doesn't cause bakanae but does cause salt damage. Tilling with water running doesn't affect bakanae.
Just one eradicating remedy should cure your rice of bakanae disease.