Yes, you can. There are two options:
1. If you set well boundary conditions with 0 values to all the nodes along the well screen, FEFLOW internally connects the nodes with an (internal) 1D finite element and forms a multi-layer well. The connection, however, is extremely conductive, corresponding to something like a well pipe with 1 m² cross sectional area and a high conductivity. So with this you would highly overestimate the flow.
2. The other option is to set a so-called discrete feature element. A 1D finite element (vertical) would be set to connect the nodes along the well screen. In this case, you can define the properties for the 1D element, such as cross-sectional area, flow law (Darcy, Hagen-Poiseuille, or Manning-Strickler), and roughness coefficient or conductivity. This would definitely be the better option, as the properties of the abandoned wells can be considered more precisely.
None of the two options, however, considers storage in the well by a moving groundwater table. Only storage by compression is considered.