I urge you to seal that room. In concrete there is very likely to be microbiological contamination, especially Listeria. If you don't have doors sealing off other areas, use polythene screening.
Before you start, plan out the works. Who will be doing them? What equipment will they be using? Where will screening go? Who will supervise the works?
During the works, supervise them and it's advisable (IMO) to take swabs outside of screening (to check it's effective but also inside screening while it's dirty. This gives you a potential root cause if an issue does occur later (and it sometimes does). Settle plates for yeasts and moulds might also be a good idea depending on your product. Ensure the work team clean up the debris.
After. When the works are done, clean the "dirty area" before reinstating as a production area and taking down the screen. After this, you may even want to think about changing your cleaning equipment or at least cleaning it thoroughly. Once the screen is down, clean it again and I mean everything. Ceilings, walls, floors. Might be worth fogging with disinfectant if possible. When you're happy the room is clean, move the kit back in then clean and disinfect that before even thinking about producing.
Ensure you record the process and what was monitored etc. Might sound like overkill but then I don't know your product but floor works are notorious for causing contamination.