Is it permissible to reside in a building constructed on land that was an endowment (waqf) and cultivated for decades, then it later became clear, during excavation for construction, that there were old graves in it which were then moved and buried in the cemetery, knowing that the seller relinquished the land at the price of ملك (mulk/private property) believing it to be private property?

You bear no sin for commencing work on land where you were unaware of the presence of graves. However, it is obligatory to return the soil over the remaining human remains and to refrain from building in the aforementioned location. If graves are found on a piece of land, it is obligatory to leave them undisturbed and not to excavate them or build upon them, as this constitutes an infringement upon the rights of the deceased. It is not permissible to exhume graves to move remains for the purpose of expanding houses. Rather, this is permissible only in cases of extreme necessity, such as for the expansion of a public road that serves Muslims and cannot be diverted. If it is certain or highly probable that the bones belong to deceased Muslims, it is not permissible to move them, and any construction must be removed, leaving the graves undisturbed.