Yeah when mine bred for the first time they did their "thing" for about an hour, then the female went and hid for a long time (approx. 45mins)...So i grabbed the net and fished her out, however, the moment i caught her several more eggs shot out while she struggled.
I have read up on the internet and most sources say it is best to leave the female in for 3 - 4hrs, unless she is being attacked relentlessly by the male.
It seems to work, i find that my female hides for long periods while the male reinforces the bubble nest with the first lot of fertilised eggs - then she re-emerges for a second and even third session. You will know when she is finally depleted of eggs because you can see that the white tube behind her ventral fins has disappeared, and she is significantly thinner than when she started.
And no, it is not bad if she dosent lay all of her eggs (unless you want the maximum yeild of fry), as she will naturally absorb the unused eggs and use their nutrients to produce the next "batch".
Joel