Same way Serbia is preventing Bosnia on recognizing Kosovo independence. Through the Serbian "entity" in Bosnia, which is, while completely autonomous internally, capable of issuing a veto on "federal" level on a range of issues, which gives Serbia leverage over Bosnian foreign policy as well a lot of internal matters.
That's actually not entirely true.
Bosnian-Serbs in RS are refusing to allow the recognition of Kosovo as it has the direct consequence of allowing RS to do the same to the BiH.. Legitimate catch 22
In your example provided on Serbia, Bosnia and Republic of Sprska. Yes much of the blame is associated with the DA (Dayton Accord), as it provided the foundation for ethnic divisions within Govt. Main problem was the limit of political diversity / structure, coupled with rampant corruption and lack of accountability.
In the case of Ukraine, the proposed lustration bill is aiming to limit Russian influence going forward, regardless of the current situation in the east of the country. If/ when an agreement is reached with the both parties and lets assumes there is a split, IMV we won't have a unique situation for another type of DA. It will be one party goes one way and vice versa.
Another point to consider is the Balkans war of the 90's, was a religious and ethnic struggle for independence, Ukraine is an ethnic issue and less divisive.
When you say 'federalisation' do you mean;
a) LNR & DNR part of the RF? (was rejected originally by Putin 5-6 months ago)
b) LNR & DNR part of a future federal Ukrainian state?