To my knowledge, up to this point I have not seen and evidence that the parents of Melchora de los Reyes(m. Luis Delgadillo) are Rodrigo de Caravajal and Melchora de los Reyes. Jaime Holcombe in his Diversas Cartas proposes an ancestry where both Melchora de los Reyes are the same person, married at some point to both Luis Delgadillo and Rodrigo de Caravajal. Jose Luis Vazquez y Rodriguez de Frias correctly states Melchora de los Reyes is the daughter of Melchora de los Reyes and Rodrigo de Carabajal in Chapter 16 of "Genealogia de Nochistlan...", however does not provide any proof. Vazquez's Chapter 79 discusses Rodrigo de Caravajal and Melchora de los Reyes (which I do not have a copy of). With the assistance of the aforementioned works, I believe I have found proof of Melchora de los Reyes parents.

Dispensa #1
https://familysearch.org/ark:/61903/3:1:9392-669W-N1?mode=g&i=263&wc=3J…

1727, Nochistlan: This dispensa is for the marriage of Joseph Diaz to Nicolasa Delgadillo h.l. of Joseph Delgadillo and Juana Yanez. This dispensa is important because is illustrates Melchora de los Reyes (m. Luis Delgadillo) is sister to Juan Rodriguez de Caravajal (important later).

Relationship disclosed:

Melchora de los Reyes..(sibling)..Juan Rodriguez de Caravajal
(m. Luis Delgadillo)..............(m. Ana Maria, indian)
Hernando Delgadillo......(2)......Melchora de los Reyes
(m. Andrea de Rodas)..............(m. Antonio de Villalobos Alcaraz)
Joseph Delgadillo........(3)......Maria Villalobos
(m. Juana Yanez)
Nicolasa Delgadillo......(4)......Joseph Diaz

Parenthesis added by me.

Thus it is proven that Melchora de los Reyes is a sibling to Juan Rodriguez de Caravajal.

Dispensa #2
https://familysearch.org/ark:/61903/3:1:9392-6V9S-89?mode=g&i=314&wc=3J…

1725, Nochistlan: This dispensa is for the marriage of Manuel Rodriguez h.l. Gaspar Rodriguez and Geronima Munoz to Ana Diaz h.l. of Sebastian Diaz and Ana Villalobos. This dispensa is important because is tells us the two children of Juan Rodriguez de Caravajal and that the mother of his children is an indian named Ana Maria.

Relationship disclosed:

Ana Maria, mother of
Gaspar Rodriguez.....(sibling)...Melchora Rodriguez
(m. Geronima Munoz)..............(m. Antonio de Villalobos Alcaraz)
Manuel Rodriguez.......(2).......Ana de Villalobos
.............................................(Sebastian Diaz)
...................................(3)......Ana Diaz

Parenthesis added by me.

Now we know that Juan Rodriguez de Carabajal had two children with an indian woman, Ana Maria.

Marriage record of Melchora de los Reyes and Antonio de Villalobos
https://familysearch.org/ark:/61903/3:1:939N-TH4S?mode=g&i=186&wc=3P9N-…

This marriage record provides further proof as it states, 19 April 1670 Nochistlan, Antonio de Alcaraz married Melchora de los Reyes hija natural of Juan Rodriguez de Caravajal.

So at this point we know that Juan Rodriguez de Caravajal had two children with an indian woman, Ana Maria, and has a sister, Melchora de los Reyes (m. Luis Delgadillo)

Juan Rodriguez de Caravajal's marriage record
https://familysearch.org/ark:/61903/3:1:939N-TH8Y?mode=g&i=217&wc=3P9N-…

13 June 1674, Nochistlan: Juan de Caravajal, single, h.l. Rodrigo de Caravajal and Melchora de los Reyes marries Ana Maria, widow of Juan Bartholome. Juan Rodriguez de Caravajal gets married for the first time after his natural daughter! Typically this would throw some red flags but his death record sheds some light on the situation.

So now we know Juan Rodriguez de Carabajal's parents are Rodrigo and Melchora, which at least one of them must be Melchora de los Reyes (m. Luis Delgadillo) parents for Juan and Melchora to be siblings.

Juan Rodriguez de Caravajal's death record
https://familysearch.org/ark:/61903/3:1:939N-TT5T?mode=g&i=38&wc=3P9K-T…

16 June 1674, Nochistlan: Juan de Caravajal, age more than 70 years, married to Anna Maria, indian. He has two hijo's naturales (3rd to last line).

So Juan dies 3 days after getting married. The two hijo naturales are Gaspar (m. Geronima Munoz) and Melchora (m. Antonio de Villalobos Alcaraz) who we know to be their mother Anna Maria. As Holcombe said "Juan married to ease his conscience"

So there you have it. The proof that the parents of Melchora de los Reyes (m. Luis Delgadillo) are most likely Rodrigo de Caravajal and Melchora de los Reyes. Additional proof can be seen based on the use of the name "Melchora de los Reyes" throughout Luis and Melchora's descendants. Luis and Melchora also had a daughter, Maria (who married Diego Moscoso y Sandoval) who used the surname Rodriguez for two of her children's baptisms.