Acceptance of applications to issue a temporary residence permit to Russian citizens is restricted. But the provision carries an exception — it does not apply to those who already hold a valid Lithuanian visa, a Lithuanian residence permit, or a residence permit issued by another EU member state.
Note the precision of the wording: the restriction covers issuing a permit, not changing one. Changing an existing permit is not caught by that provision.
That said, a change still goes through the general security assessment, which is where most negative decisions are made.