Can a smaller company (R&D unit) owned by a large enterprise that is a beneficiary/partner in the project be a linked Third Party?

It can be a Linked Third Party if it is under the ‘direct or indirect control’ of the beneficiary. This means that the large company must (directly or indirectly) hold of more than 50% of the nominal value of the issued share capital, or a majority of the voting rights, or the decision-making powers in the R&D unit.EQT Support Boost