Is a prayer against one who did not deliberately do wrong answered?

Firstly:

It is not permissible for a Muslim to accuse another Muslim, man or woman, of stealing except if the thief admits it or there is valid evidence; evidence may be based on the testimony of two men of good character. According to some of the scholars, proving theft may also be done on the basis of clear circumstantial evidence.

It says in al-Mawsoo‘ah al-Fiqhiyyah al-Kuwaitiyyah (24/332): The fuqaha’ are agreed that theft may be proven on the basis of a confession or proof. According to some of them, theft may be proven by the accused’s refusal to swear that he did not do it [whereupon the accuser is called upon to swear that the accused indeed committed the theft]; according to others, it may be proven on the basis of circumstantial evidence.

Confession is where the thief admits his deed, if he is accountable in the sense that he is an adult of sound mind. The majority of fuqaha’ are of the view that the thief must give his confession willingly; if he is forced to confess by means of detainment, beating and the like, then this confession does not count.

With regard to proof, it is the testimony of two men who fulfil the conditions of bearing witness. The testimony of one man cannot be accepted, even with an oath sworn by the one from whom property was stolen.

With regard to circumstantial evidence, the majority of fuqaha’ are of the view that the hadd punishment for theft cannot be carried out except on the basis of a confession or proof.

Some of them narrated that it is permissible to establish theft and hence carry out the hadd punishment and establish liability for the stolen property on the basis of circumstantial evidence and other signs, if the signs are clear, on the grounds that this helps to restore the rights of the one who has been wronged.

Ibn al-Qayyim said in at-Turuq al-Hukmiyyah (p. 8):

Governors and caliphs always ruled that the thief’s hand was to be cut off if the stolen property was found with the accused, because this circumstantial evidence is stronger than proof or a confession; a proof or confession may be true or false, whereas the presence of the property in the possession of the accused amounts to clear evidence that is not subject to any doubt. End quote.

So long as there is no confession from the [alleged] thief, and no valid evidence such as finding the stolen property with him, then it is haraam to accuse him of stealing, and accusing him is obviously wronging him.

Allah, may He be exalted, has commanded us to avoid suspicion or negative assumption, and has warned against wronging others and accusing them of things of which they are innocent. Allah, may He be exalted, says concerning the former (interpretation of the meaning): “O you who have believed, avoid much [negative] assumption. Indeed, some assumption is sin. And do not spy [on each other]…” [al-Hujuraat 49:12].

It was narrated from Abu Hurayrah (may Allah be pleased with him) that the Prophet (blessings and peace of Allah be upon him) said: “Beware of suspicion, for suspicion is the falsest of speech. Do not seek out the faults of others; do not eavesdrop on others; do not hate one another; be brothers.” Narrated by al-Bukhaari (4849) and Muslim (2563).

Al-Qurtubi (may Allah have mercy on him) said: What differentiates the suspicions that must be avoided from other thoughts is the fact that every suspicion for which you know of no sound indication or clear reason is haraam and must be avoided. That applies if the target of the suspicion is someone who is known to be decent and righteous, and appears outwardly to be trustworthy. In that case, assuming him to be an evildoer and treacherous is forbidden.

End quote from Tafseer al-Qurtubi (16/331).

Allah, may He be exalted, says (interpretation of the meaning):

“And those who harm believing men and believing women for [something] other than what they have earned have certainly born upon themselves a slander and manifest sin”

[al-Ahzaab 33:58].

The Messenger of Allah (blessings and peace of Allah be upon him) said: “Beware of injustice, for injustice will be darkness on the Day of Resurrection.”Narrated by Muslim  (2578).

See also the answer to question no. 112196, in which there is an explanation of how the Muslim may avoid thinking ill of people.

Secondly:

If your maternal uncle did not have any evidence or clear proof concerning which there could be no doubt to prove that the servant is the one who stole something, then in that case he has wronged her, and Allah has promised to support the one who is wronged and to answer his du‘aa’ (supplication).

The Prophet (blessings and peace of Allah be upon him) said: “There are three whose du‘aa’ will not be rejected: a just ruler, a fasting person when he breaks the fast, and the prayer of one who has been wronged. Allah will raise it above the clouds and the gates of heaven will be opened for it, and the Lord, may He be glorified and exalted, will say: ‘By My glory, I will grant you help even if it is after some time.’”  Narrated by at-Tirmidhi (2525); classed as saheeh by al-Albaani in Saheeh at-Tirmidhi.

This hadith indicates that it is permissible for the one who has been wronged to pray against the one who wronged him, but he should not pray against him except on the grounds that he has wronged him or overstep the limits in his supplication, so that he himself wrongs him.

For more information, please see the answer to question no. 71152.

But if your uncle has proof or circumstantial evidence that is strong enough to indicate that she stole it, but in fact the servant did not steal anything, then he is excused for accusing her, because there is some ambiguity about the matter.

What appears to be the case – and what is hoped for by the pardon and grace of Allah – is that Allah will compensate her from His generous bounty and console her thereby, and that He will compensate her for the wrong done to her, or more, and that He will not answer her prayer against your uncle, because he did not deliberately intend to wrong her and he did not fall short in striving to ascertain the facts of the matter and preserve the rights and dignity of the accused, so he is excused if he adhered to the guidelines set out by Islamic teachings in verifying circumstantial evidence. And Allah is the Knower of the unseen.

And Allah knows best.