IMHO, Davis still had a Beauregard burr under his saddle when Davis wanted him for Bragg's replacement and Beauregard had left for recuperation of some sort. This was just after Shiloh.
O R Vol 17, part 2
Richmond, Va., June 14,1862. General Braxton Bragg, Tupelo, Miss.: You will immediately proceed to Jackson, Miss., and temporarily assume command of the department now commanded by General Lovell. After General Magruder joins, your further services there may be dispensed with. The necessity is urgent and absolute. JEFFERSON DAYIS.
Tupelo, Miss., June 14,1862. (Received at Richmond, Va., June 15,1862.) General S. Cooper: General Bragg has just communicated to me a telegram sending him to relieve temporarily General Lovell. His presence here I consider indispensable at this moment, especially as I am leaving for awhile on surgeon's certificate. For four months I have delayed obeying their urgent recommendation in that respect. I desire to be back here in time to take the offensive as soon as our forces shall have been sufficiently organized. I must have a short rest. G. T. BEAUREGARD.
National Archives
6/14 Davis technically violated military etiquette when he directly ordered Bragg to relieve Lovell in Jackson w/o at first consulting w/Beauregard, Bragg's superior. Davis concluded by telling Bragg that after Gen Magruder joins, your further services there may be dispensed with. The necessity is absolute & urgent.
On that same day, however, Beauregard turned the army over to Bragg & prepared to leave for Bladen Springs near Mobile.
Bragg could not go to Jackson Beauregard telegraphed because "I must have a short rest."
6/14 Bragg to Davis-order rec'd & will be obeyed promptly
6/14 Tupelo, Beauregard to Davis- Gen Bragg has just communicated to me a telegram sending him to relieve, temporarily, Gen Lovell- His presence here I consider indispensable at this moment, especially as I am leaving for a while on surgeon's certificate. For four months I have delayed obeying their urgent recommendations in that respect. I desire to be back here to retake the offensive as soon as our forces shall have been sufficiently reorganized. I must have a short rest.
6/16 Davis to Bragg-My telegram to you was so absolute & for such immediate action that I hope you have not permitted yourself to be interfered with in the execution of the order. The value of your presence depends mainly on its being immediate. It was not expected to be more than a temporary arrangement
6/ [17] Bragg to Davis –telegram from Tupelo-got yours of 16th-reports Beauregard left this army today for Mobile & Lovell has returned to Jackson thus it would be very unfortunate for this army if I leave now-asks instructions
6/19 Davis to Bragg-disappointed that order not executed, particularly since time is so important-Send Van Dorn with all possible dispatch to assume command of the Dept of S Miss & E La. - A temporary assignment