If "One aliquot can only be part of one batch at all" then the description would be "One aliquaot can only come from one single batch.
An aliquot may be sampled from or used in one batch only. "An aliquot can only be taken or sampled from a batch once." or "An aliquot can only be used in a batch once."
An aliquot is contained an exact number of times in a group or batch or collection. Such as one of a dozen. You can have two eggs of a dozen but not 1.75 of them. Having divided the quantity you can only choose a discreet number of them, a number of aliquots. For your use you are restricting the choice to only one aliquot of the collection. 1/12 or 1/X not three or four of the batch.
Since you are referring to batches of chemicals from which you take samples the discrete number part of aliquot may not apply though the word is still used. A sample taken may not be quite an exact quantity. What you are trying to capture is the idea that the sample's nature includes where it is from and where it goes, what it might become after some process is used. Which of these two it is doing is unclear.
"One aliquot can only be part of one batch at all"
"One aliquot may be part of multiple batches"
This depends on where each is going to or coming from. "One aliquot can only be added to one batch ever" or "One aliquot can only be taken as a sample from one batch ever"
If you could fill in a bit more detail I'm sure the answer would pop up here shortly. Apart from that I would say "An aliquot can only be taken or sampled from a batch once." or "An aliquot can only be used in a batch once."