Yes and no. Ideally, substitutions should be decided on ahead of time (so one doesn't "fish" for preferred scores or profiles). However, substitutions can also be made on the fly, or after the fact, if it is determined that a core subtest is "spoiled". For example, (and this has actually happened to some of us!) if an unannounced fire drill happens in the middle of one of the working memory or processing speed tests, there would be good reason to believe that the resulting score is not fully representative of the student's ability. In that case, a post facto substitution is allowed. I have also made substitutions after the fact, judiciously, based on extremely divergent performance between core subtests, but I always take care to provide interpretation that explains my reasoning for doing so, and what I think the divergent subtest scores may represent.
Planned subtest substitutions are usually based on points such as,
1. Additional measures of verbal reasoning may balance effects of differences in exposure to verbal materials, so Word Reasoning might give a better picture of reasoning, with less confounding from vocabulary effects.
2. Motor deficits are suspected, so Picture Completion is substituted for Block Design, to create a completely motor-free PRI.
3. There is a view that Arithmetic is a better representation of working memory than Letter-Number Sequencing in GT children.
4. Cancellation is substituted for Coding, to create a motor-reduced PSI.
When I make such substitutions, though, I administer the original core subtest as well, to test the hypothesis.