It seems to be a maximal clique problem. The larger the clique (subset of vertices- orders with a common storage area as edge) smaller will be number of storage areas covered.
Seems there's no straight forward algorithm possible in polynomial time but a Bron–Kerbosch algorithm has been referred.
Other than that using my simple OR skills I can try an MIP & set covering technique.
Define set of batches $B$ of same cardinality as number of orders $O$ because that's the maximum batch possible
Define multiple sets $S_o$ as the set of storage areas $s$ from where order $o$ can be picked. It can be a matrix also as $M_{s,o}=1$ if order can be picked from a storage area, else $0$
Optimization variable:
Binary $x_{o,b}=1$ if order $o$ is assigned to batch $b$, $0$ otherwise.
Binary $y_{s,b} = 1$ if storage $s$ is covered by a batch $b$,
Binary $z_b = 1$ if batch $b$ is chosen
Constraints
$ \sum_b x_{o,b} = 1 \quad \forall o$
$ z_b \le \sum_o x_{o,b} + \sum_s y_{s,b}\le C_bz_b \quad \forall b$: where $C_b$ may be a batch capacity in terms of orders or storage. You can split it also into one for constraining number of orders per batch & another with $y$ ensuring no storage is included in a batch unless batch is chosen
$ y_{s,b} \le \sum_o M_{s,o}x_{o,b} \le Ty_{s,b}$
where $T$ is a big number like $O \times S \times B$
$ x_{o,b} \le \sum_{o' \in O \setminus o}\sum_{s} M_{s,o}M_{s,o'}x_{o',b} \quad \forall o, b$
Or
$ x_{o,b} \le \sum_s M_{s,o}y_{s,b} \quad \forall o,b$
Basically trying to constraint any order from being assigned to a batch if it doesn't share any storage area with any of the other orders
Objective
$\min \sum_{s,b}y_{s,b} $
Another way - TSP:
@Ying multiple shared storage areas imply multiple edges (multi-graph). There will be algorithms for clique creation for multi-graphs. Otherwise you can define your own heuristic.
You can also try with Travelling Salesman problem (TSP): visiting all nodes covering minimum number of edges (storage). Typically in TSP sub-tours (batches of nodes) are eliminated. Here you may preserve subtours.
needs to be picked from multiple storage areas
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