Batch and lot traceability shouldn't vary too significantly between "agile" and standard storage and operational movements.
API can easily receive a barcoded label in either a 1D OR 2D format. The barcode will indicate product information related to lot/batch, dating, and product information. This barcode can then be used to locate the product in a physical location or a systemic location. The API can be assigned to its finished goods batch now or later and when the API is needed, a task can be generated by the ERP or WMS to retreive the product and bring it to where it is needed.
Likely company processes associated with finished goods storage, particularly related to cold storage and DEA product as well as serialization could be leveraged here.

Can you please elaborate a little bit more on ther batch production? An usual lot number doesn´t work properly?

There's a lot of small software companies out there that can produce low cost bespoke packages to do exactly this. Get what you need tailored to your requirements.

I am amazed how often folks ask a question that a simple INTERNET search would answer. An answer to the batch question can be found on several websites, for example
http://www.who.int/medicines/areas/quality_safety/regulation_legislation/certification/guidelines/en/index6.html
"*Batch (or lot): A defined quantity of a starting material, packaging material, or product processed in a single process or series of processes so that it can be expected to be homogeneous. In the case of continuous manufacture, the batch must correspond to a defined fraction of the production, characterized by its intended homogeneity. It may sometimes be necessary to divide a batch into a number of sub-batches, which are later brought together to form a final homogeneous batch.
Batch certificate: A document containing information, as set out in Annex 3 of the Guidelines for use, will normally be issued for each batch by the manufacturer. Furthermore, exceptionally a batch certificate may be validated or issued by the Competent authority of the exporting country, particularly for vaccines, sera and other biological products. The batch certificate travels with every major consignment (see also item 3.14 of Guidelines).
*Batch number: A distinctive combination of numbers and/or letters which specifically identifies a batch on the labels, the batch records, and the certificates of analysis, etc.

I would also suggest automating any of these processes at every stage. The companies that I have worked with that manage inventory well, standardize, automate and then replicate those processes across operations.
This provides for scalability as they grown or acquire new products and units. It also means they have data and visibility and can manage the operation much for effectively while applying analytics and data modeling for scenario planning. This will improve everything from quality sampling, compliance and batch record management to working capital and ease of financial close.