If you plan on having the floor finished,I'd just leave it up to the floor finishers to fill everything.They will likely have the appropriate filler,which is imperative.You want to use something that dries fast,and is sandable.I prefer Woodwise for Oak,pine,maple and cherry flooring.With big cracks/holes,it will likely be necessary to "re-fill" several times,as the filler will sink until the crack is full. I use a 4" putty knife,and fill one crack at a time,going back and forth mashing the filler in several times.It may seem impossible,but if you hustle,you'll be surprised how fast you're done.Trowelling is the fast way,but with large cracks you may end up doing it 3 times...that's a lot of filler. You should also consider the RH conditions,moisture content,etc.If you anticipate any excessive movement in the flooring,you'll likely vacuum the filler right up out of the cracks.I always try to leave enough of the smaller cracks open to allow for a bit of expansion.
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