should i cut the dark stems?

i got a string of pearls a while ago and it looked so good but then i noticed it had thrips 😭 the soil was also staying quite moist which i hadn't noticed but i decided to repot it into a terracotta pot with 1/2 of cactus & succulent potting mix & 1/2 of perlite. because the roots are quite fragile and the soil was moist, i probably lost quite a lot of tiny roots. but a lot of the stems still had decent roots. i also rinsed them with water (i've heard that these don't really like getting wet but they had some soil on them and i was going to use a pesticide so i thought it would be wise) and after that i sprayed then with substral pesticide spray that works on thrips. after that i put a plastic bag over the plant because i had came across that tip multiple times. later i found out that it probably wasn't a great tip. luckily i only kept it on overnight or a day or so. a lot of the pearls turned mushy and some of them have just died/dried out. i lost a lot of the plant which i'm devastated about but i'm now trying to save what's left. the stems still have nice and long roots, but many of the stems have brown/black areas before the pearls or in between them. i'm wondering whether they are functional or whether my best bet is to cut them. many of the dark spots are before the pearls so many of the stems wouldn't have any pearls left after cutting even though the roots are good. but if the stem is dead or not functioning, are the roots useless? i'm also scared i won't be able to root the cuttings if i decide to cut them 🙁 so what do i do? i already took one or two cuttings from stems that had pearls before the black areas.