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Need advice to save corys

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I've had some False Julii Corydora for about 6 months. After a couple months I noticed some mild barbel erosion on a couple of them but it seemed to stop progressing. Recently it started up again and accelerated very rapidly to the point their barbels are mostly gone and one has a severe lesion (developed over a couple days) where his barbels were and seems to have stopped eating with the others.

After doing more research (which I should have been more thorough with earlier), I know I should not have put them in with my Eco-complete substrate. I feel absolutely terrible about that. Also, the fact that it took a while for erosion to appear but then accelerated so rapidly makes me think there may be some infection involved as well. Some of the reading I've been doing supports that possibility as well.

My first question: is this something they can likely recover from and still have happy lives?

Here's what I've done to try to get a little quick relief for them:
  • Started putting food in small glass dish to reduce scraping and keep the substrate cleaner. They seem to like this
  • Frequent and thorough substrate vacuuming to keep it cleaner
  • Increased water change frequency

I still need to change the substrate and try to treat any potential infections, but I need some advice:

In switching the substrate would it be less stressful for the fish to take them out or try to replace it in-place without removing them? I'm worried about stress weakening them if they are already compromised by infections.

For a new substrate I'm debating between sand or extra fine grain Marfied Controsoil (1mm grain size). I've read really good things about the Controsoil including that it doesn't have an initial ammonia spike like ADA Aquasoil does. Has anyone used it with corys?

Finally, how can I tell if they have an infection that is making it worse and if so what it is so I can try to treat it? I've read that people have seen rapid barbel erosion caused by flukes. How would I diagnose and treat that?

Any advice would help. Thanks!
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· Children Boogie
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It's not the substrate per se but the bacteria on it that's the issue. Clean water, gravel vac lightly, and a round of antibiotics should help.

I've never had barbel issues unless I don't change the water periodically.
 
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