which 在这里指代的是什么？还原后in 在什么位置？

不可以。如果是the process that water diffuses from a higher to a lower concentration 那句子就不完整，仅是the process和其同位语，没有其他成分

the process in which water diffuses from a higher to a lower concentration
还原后是
water diffuses from a higher to a lower concentration in the process

不可以。
这里in后面的宾语是定语从句中的关系代词which，表示“在这个过程中”的意思，如果去掉意思成了“这个过程”，与原文意义不符。

这里不能换成that,因为介词提前到关系代词前面时只能用which，不能用that。但是如果把in放到距最后就可以改为that了。

which代process

e.g
This is the house in which i once lived.

原句可变为
water diffuses from a higher to a lower concentration in this process. in不能省略

不可以
the process 是物,定语从句引导词可以用that或which,但有介词in,只能用which
改为the process that water diffuses from a higher to a lower concentration in

不可以改成 the process that water diffuses from a higher to a lower concentration
process必须有介词in
in 放到最后就可用that,因为that不可以和介词in放一起