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Unfortunately, if the stem has already softened and become semi-transparent, that's really a sign of rot. Two days in water for a cactus is like us spending two days in a downpour. Its roots simply can't survive that much moisture - they become waterlogged and die, and the rot starts creeping up the stem.

But don't lose hope completely. Cut away all the damaged areas with a sharp knife down to healthy tissue - it should be firm and not transparent. If the rot has spread high up, you can remove the entire soft top, leaving only the strongest part. Let the cutting you've removed sit in the shade for a few days so the cut dries out and a cork layer forms over it. Then plant it in completely dry cactus soil and don't water it at all for the first month - just mist the air nearby if things get really critical. New roots will appear gradually.

It's possible nothing will be saved, but a cutting like this has pretty good chances. I once saved a huge overwatered cactus this way - the top took and grew back, though I had to wait a long time for it.

The main thing now is to let the cactus dry out, but it's already too late to save the roots if they've been in water for two days and the stem has started to soften. Softening and semi-transparency - that's rot, and it's already starting to develop. You need to cut away everything that's affected down to healthy tissue with a sharp, clean knife or blade. Healthy cactus tissue should be firm and light-colored on the cut. Cut into the living part - a new plant can grow from that later.

After cutting, let the cuts sit in a dry place for 5-7 hours so they dry out and seal over. Then plant it in completely dry, loose cactus soil (or make your own from equal parts sand, perlite, and soil). The pot needs drainage, and for the first two weeks don't water it at all - just mist the air around it if it's really hot. Bright light but not direct sun, temperature above 20 degrees.

Even if the cactus looks rough after cutting, that's normal - the important thing is that the remaining part can develop roots and recover. Start watering only after a month, just a tiny bit, and only if the soil is completely dry. Cacti are very vulnerable to rot again during this period.

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