According to the Electoral Count Act, in order for a slate of electors to qualify for “safe harbor”, the electors must be chosen according to the laws of the state enacted prior to Election Day (November 3), and any/all disputes related to the appointment of electors must be resolved at least 6 days prior (December 8) to the meeting of electors (December 14). 3 U.S.C § 5.
Congress usually shows deference to slates qualifying under the “safe harbor” protection, and as long as there is a single slate from a particular state, and there is no allegation of corruption, the slate would be counted.
A slate would fail to qualify for the “safe harbor” protection, if either the electors were appointed in contravention to the election laws enacted prior to the Election Day, or if the disputes were not resolved six days prior to the meeting of the electors.
If Congress does not object to counting the votes from a slate that did not qualify for “safe harbor” (provided there was a single state presented from the state), there is no problem and the votes get counted. However, if Congress objected to counting votes from a slate that did not qualify for “safe harbor,” and there are multiple slates from a state, then the Congress would have to decide on which slate to count.