The whole point of the tongue and groove in flooring is to allow for each board to expand and contract normally through the seasons, yet not show major gapping or tenting that square edged boards would. A tight fit or filler is anathema to that, and will lead to buckling or fill fall out.

If you just want to clean the dirt accumuated in the grooves, then mineral spirits and an old toothbrush and soft cloth will do that. But test to be sure that it is compatible with the finish. Unless you are planning to sand and refinish after renailing.

This will be a TON of work to do, so you really need to examine exactly how much thickness of the wood above the tongue really remains. If the floors only have one sanding left, then this is really wasted effort. Reuse them as something other than flooring.

Is 100 yr old oak flooring really going to measure 3/4 x 2 1/4"? Seems like modern dimensions to me.

Thanks Sophie! I have read that putty or filler would come out in a year but I didn't know it could buckle the wood. I'm not a fan of that anyway, hence my trying to clean it properly for a nice install.

I will try mineral spirits on a test board and see how it turns out. I just didn't want to do anything too harsh that would damage the edges.

Our wood is actually 14/16th's as of today, so we have plenty of wood left to sand. Thanks for the heads up!

Mineral spirits is going to take forever, and chances are wont get it clean. If you want them clean, its going to require scrapping the gunk off the tongues and sides. When ever i tear out some exsisting and use it to patch an older floor, its what i do. its faster then sitting there scrubbing away. its elbow grease but it works.

As far as wood filler goes. It all depends on the type of filler used. I've never seen a floor buckle because of filler. Todays filler doesnt harden to solid rock. good stuff will remain flexiable to move along with the wood.

cleaning up the floor before installing will lessen the amount of filler in the floor, but because of the age, it may still require some to hide some imperfections.

And to determine the age or how many sandings the floor is capable of is determined by the measurement of wood above the tongue.

If you have finish bonded to the edges, an application of paint stripper will help loosen it before scraping.

Thank you! I have a new scraper and will try all of the tips suggested to see what works best for the gunk on our wood!

"I will try mineral spirits on a test board and see how it turns out. I
just didn't want to do anything too harsh that would damage the edges."

Don't worry about damaging the edges ...that stuff's tough.

I clean the grooves with a chunk of strap iron with the right profile - I don't remember where I got it, but it's rounded just right for shoving out the dirt. You could use a bent bolt of the right diameter or any other tool.

I scrape the edges of the tongue with a dulled chisel to get rid of decades of floor wax and spilled crud.