what can be singular or plural in number. When using it to ask a person's favourite fruit, it takes a singular verb. The assumption here is that "favourite" implies one, not two or three, so "What is your favourite fruit". If more than one favourite fruit, then "What are your favourite fruit(s)?, wherein What is plural in number:
Question: [b]What are[/u] your favourite fruit(s)?
Answer: Strawberries and bananas are my favourite fruit(s).
Question: What is your favourite fruit?
Answer: Strawberries are my favourite fruit.
Answer: Bananas are my favourite fruit.
Why the plural nouns, Strawberries, Bananas? Well, when talking about one's likes and dislikes, a plural noun is used:
 I like bananas.
 I like banana. <ungrammatical>
The implication is that one likes all bananas, not just one.
If you want to specify a specific fruit among the class Fruit, use the determiner "the":
Question: What's your favourite fruit?
Answer: The banana is my favourite fruit.
Notice the word order above. Instead of answering, "My favourite fruit are bananas" or "My favourite fruit is the banana", we've switched the subject "My favourite fruit" and the subject complement "bananas / the banana."
 My favourite fruit is bananas. <"fruit" agrees with the verb>
 Bananas are my favourite fruit. <"Bananas" agrees with the verb>
The reason for the switch is twofold. (1) example  is copular in structure: Y = X or fruit = bananas. Structurally, a singular noun "fruit" equals a plural noun "bananas". Is that correct? It sounds wrong, but it's not. (2) "fruit" is not a subset of bananas; it's the other way around. Bananas are fruit. Fruit are not bananas, and the reason most speakers switch the word order. It's easier grammatically, as well as semantically to place the subset before the set's name:
Bananas are my favourite fruit.
As for your second question, the infinitive verb "to be" has been omitted in the sentence. That often occurs in Modern English. The full form is,
'If you would like the windows to be changed we can do it for you.'
The word 'changed' is a past participle in form.
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