My friend is going to board into the train.
To give a sarcastic sent off… shall I say,
"Make sure your train doesn't derail"
Is "doesn't" appropriate here?
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This is an example of an error in Modern English that is now accepted. Prior to this, in the sentence above, the present subjunctive would have been used. A very correct form would be:
Make sure [that] your train not derail.
Many native English speakers who hate the sound of the present subjunctive, but also don't like the present tense sound in this instance, will use a modal herein "to try to preserve some semblance of" the subjunctive:
Make sure [that] your train should not derail.
Make sure [that] your train shall not derail.
Make sure [that] your train will not derail.
Make sure [that] your train might / may not derail.
The reason it should be the present subjunctive above is because "make sure" means "see to it".
"See to it that your train not derail."
In English, "see to it" is usually followed by a subjunctive. When "make sure" means "check to see whether" or "check whether", then there is no present subjunctive used. For instance:
Make sure that John has his homework done. (This means "check to see whether John has done his homework.")
Make sure that John have his homework done. (This means "see to it that John have done his homework (by the time I get home).")
Here are some good examples that I've listed in the comment section, but that I want to add to my answer to show this concept better:
"I will see to it that he be hanged for his crimes!"
"I'll see him [be] hanged for his crimes!"
"I'll make sure that he be hanged for his crimes!"
"It is important that he be hanged for his crimes, so let him be hanged!"
"So be it!" (i.e. "So be he hanged" or "So shall he be hanged")
Now, what I am telling you is technically-correct English; however, very few native speakers of English follow the rule I've state above. It is the rule, however, because I've researched it as I, too, have asked the same question. The present subjunctive in Modern English doesn't get much éclat, so that's the reason that "doesn't" is often used in this situation.