Good question. The difference is very subtle and a bit tricky to explain. Let me show three variations that are all correct and describe the small differences.
1. The purified juice is boiled in an evaporator to remove water so that it can be concentrated into the syrup.
This would be correct if you'd previously referred to the syrup, and boiled juice was being added into the syrup as an additional ingredient. It sounds like that's not the case here though.
2. The purified juice is boiled in an evaporator to remove water so that it can be concentrated into syrup.
vs.
3. The purified juice is boiled in an evaporator to remove water so that it can be concentrated into a syrup.
Both are correct, and both sound natural. There is a very subtle (maybe 1%) difference in meaning, though. Usually adding "a" or "the" like this would make the sentence refer to a specific item, but in this case it's a little different. Without "a", this is describing "syrup" as a specific thing that the juice is directly converted to. With "a", it suggests that that juice is converted to a syrupy substance/texture. This subtle difference works here because the word "syrup" is ambiguous and refers to many different kinds of thick, sweet liquids.
Let's look at another example that works differently:
The oven converts the ingredients into cake.
vs.
The oven converts the ingredients into a cake.
Again, both are correct, and both are very similar. But here, adding "a" has the more typical effect of referring to a specific/single cake.
Last point: Consider the difference between the following:
The purified juice is boiled in an evaporator to remove water so that it can be concentrated into syrup.
vs.
The purified juice is boiled in an evaporator to remove water, which concentrates it into syrup.
The first option ("so that it can be") implies that concentration is a second step that comes after boiling.
The second option ("which") is correct if the act of boiling directly turns it into syrup.
