Like Karolus said, earlier on, i.e. in the 15th century, Portugal didn`t have such bad chances.
In the OP, you also asked about consequences elsewhere, e.g. for the colonised peoples.
I think a devastating and exhausting war during the right time frame (1430s-1450s) could indeed abort the whole Portuguese discovery boom.
Imagine Henry the Navigator having to dedicate all his resources to inner-Iberian warfare, and likely being killed. Imagine no caravels developed.
OK, so peeks into Africa may not be able to be butterflied, but I think if you`re placing a big war right in that time frame, you`ll likely kill any Iberian discovery of North or South America in the late 15th and maybe even early 16th century.
The question is why would the two kingdoms go to such an irrational war against each other.