Cut them, they will cause you nothig but grief. the spots that are dry didn' colonize (told you!), spray them with steril water, if they ar not too big, dig them out to the point where you reach mycelium, you can case over the surface but you risk infecting the casing UNDERNEITH - so it wil gro in huge unseen matts that will surface and will be impossible to control using tradional methods - also it will put spores into your atmosphere at alarming rates. I'd wait, the rest of yours substrate is fine, it is in no danger. You made those holes too big didn't you - you were afraid that it wouldn't get enough air.
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Be willing to chuck everything and clean your room up if you see more than a few spots of contam, especially early on, you will be fighting an uphill battle that you are unlikely to even draw to a standstil. You migh get a yeild, but not even close to what they work you pu into it deserves.
No, I still haven't even opened those yet, no polyfill. But that's ok, I can give them a bit more time and then cut it out if required.
I'll chuck the contamned one, not a problem.
I don't like contams. This are my 1st bins to go, but my previous location was a LOT cleaner.
I've bought 8' high white plastic sheeting. I wrapped it in 1x2s and nailed it into the ceiling, creating 2 x 10 foot draped plastic hallways leading to my glove room. I will secure it in, and use it to create multiple clean (not sterile, but dammit, they will be CLEAN) spaces (with airlocks and booties) for substrate layout and then growth.