I have a homestead patent file for 160 acres in Southern Oregon that notes the final application approval was held up for over a year due to a conflict with the 1866 O&CRR grant. There is one letter in the file from the local land office to the GLO in Washington, D.C., mentioning the patent was delayed due to this conflict, notification was given to all parties, and no appeal was received. The patent was ultimately awarded to the applicant in 1884.
If there is additional correspondence/documentation regarding the conflict with the grant location lines and this patent, would it be best to check in 49.3.7 Records of Division "F" (Railroads, Rights-of-Way, and Reclamation Division)?