We consider a problem of allocating Virtual Network Functions (VNFs) in 5G networks, treating it as a multiple multidimensional knapsacks reconfiguration problem where items represent VNFs and knapsacks represent servers on which VNFs are able to run. Given an initial and final assignments of items to knapsacks, the task is to define a sequence of steps for moving items from a source knapsack and/or to a destination knapsack. The objective is to minimize the total number of steps in which items are not in the knapsack, which reflects the total time that VNFs are not operational. We derive a non-compact formulation and a new compact formulation of the problem, and evaluate their performance with numerical experiments.