Can I use a difference score as the dependent variable and use the baseline score as the independent variable when doing correlation, linear regression and multivariate linear regression? Thank you.
If the variables are measured less than perfectly, this is a bad idea because you will be predicting the error of the baseline measure. E.g. suppose person 1 had a "good day" at BL and person B had a "bad day". Then, even if neither changes, it will look like they did.
You should use a multilevel model.
Given you have the same thing measured twice you could either do
lm(y2 ~ y1 + x, data = df)
or treat it as multilevel/repeated measures to account for the nesting of the two occasions within subjects as @Peter Flom noted)
m1 = nlme::lme(y ~ x, random = ~ 1|SID, data = df)