As long as the Transformation is not replacing an attribute of the index on which the Transformation condition's are based on, it should be safe to use.
For example, if you are looking to transform your product's size attribute from numbers like 6,8,10,12 to letters like S, M, L, then you need to make sure you are creating a new attribute instead of replacing the existing one. Replacing the attribute will cause an issue the next time the transformation will run, as it will be on the already transformed data.
You need to make sure that your transformation can run multiple times without breaking your records.