Conclusion: this practice is completely acceptable.
I believe this is generally what occurs when you have an immutable object. Instead of mutating the original object, a new one is created with the given value and returned. The arguments for and against doing this with method chaining are roughly the same as using mutable vs. immutable objects.
The only concern I would have is that this is made clear to the callers of the class - they cannot depend on identity equality with the chained object and it must be made clear the call is not changing the original object. Although if they were actually chaining the calls, they would not be assigning the intermediary objects, so there wouldn't be much of a risk of this. What's important is that they only use the last object in the method chain.
To use java.lang.String as an example, a client of String doing this:
myString.trim().replace("a", "b").substring(3, 9);
... means nothing, and generally indicates programmer misunderstanding. What they should be doing is this:
String myNewString = myString.trim().replace("a", "b").substring(3, 9);
... and then using myNewString
in subsequent operations. Interestingly, the static analysis tool for Java, Findbugs, can detect instances of this misunderstanding, and report it as a probable bug.
Client understanding is the main case. Other drawbacks include if the value object is very expensive to create, making a new one on each chain will be a performance hit. You should be able to tell from your own scenario if this is likely to be an issue. In this case, rather than creating a new object on each method chain, you may want to implement the Builder Pattern.
Apart from those, I can't think of any other issues.