Even if they 'arrest' you, they will still have to detain you in some kind of a facility, something unlikely to be a part of any embassy, and that's assuming they even have the personnel available to conduct such an arrest and detention. Also, they still have to transport you through Romanian territory to Syria. Whether or not you have sought protection, that would require some kind of agreement between Syrian and Romanian authorities to allow that to take place. There is an extradition treaty between Syria and Romania, but that is for crimes of a very serious nature and I'm not sure how that applies anyway since you would have been arrested by, and in custody of, Syrians.
No. I think your biggest issues are:
If they would issue you another passport at all (some countries deny passports to those accused of crimes).
Whether letting the embassy know your location would not invoke a response from Syria asking Romania to take you into custody and extradite you.
As mentioned in the comments above, if you have applied for refugee status in Romania because you fear persecution from the Syrian government, then you would very likely lose that status (or relinquish the claim thereof) if you avail yourself to that same Syrian government for consular services.