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If rdot is a symbolic variable and r a symbolic function, eq.subs({rdot: diff(r(t), t)}) should work. For example:

sage: rdot, t = var('rdot t')                                                                       
sage: eq = rdot^2 - 3*rdot                                                                          
sage: r = function('r')                                                                             
sage: eq.subs({rdot: diff(r(t), t)})                                                                
diff(r(t), t)^2 - 3*diff(r(t), t)