Only the lessons you manually create in the substitutions or lessons you move, can be directly deleted using Tool/Remove:
The substitutions lines that are created because someone was absent cannot be simply releted. If some teacher is missing and he is teaching certain lesson, you have to do something. Either cancel this lesson, or assign another teacher.
The only way to remove the substitution is to remove the original teacher from the list of absent teachers(or adjust the from-to if he/she is absent on part of the day only).
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