For the microplastics issue, it does depend, as you've said. The material is to blame: while some fabrics are made purely of wool, linen, cotton, silk, etc. some are made of a percentage of polyester or other plastic-based fabrics. When you wash these, they'll release the microplastics as the fibers are damaged with each wash. This damage will happen whether you're using the purest most natural fabric or the most plasticky shein cloth. It's part of the natural wash and wear cycle of clothing, though careful handling goes a long way.
The problem with the bought filling is just that: it's mostly polyester, and the fibers are tiny, loose and moving around. So, they'll shed microplastics quickly. If you use cotton threads from the scrap fabric you used, for example, they'll be filling out the plushie, but not as softly as poly fill. However, they won't leak microplastics.
After a lot of rough use or maybe even decades of love, the plushies might need more filling, yes. However, they'd need to be loved to BITS for this to happen. So, yes, you might have to replace a bit of filling after a few years. You only need a seam ripper, and a needle and thread. This will be enough to replace it.
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