Regarding the 5E rulebook - that is based only on a typo(?), as the short paragraph they are mentioned in gives the number of Major Orders with four instead of six, hinting at the destruction (or retconning) of the remaining two, and with them about 8.000 Sisters. I don't know where that "90%" is supposed to come from, unless someone for some reason assumed that there were millions of Sisters before, as the paragraph also hints at a comparative rarity.
It is worth mentioning that the missing two Orders were again mentioned in the new WD Minidex, so I suppose that line in the 5E Rulebook was either a mistake, or whoever wrote the WD 'dex didn't pay attention. The former would seem more likely, of course.

Brother Coa wrote:I see, so until the new Sister codex we won't know anything about their numbers. Since 5'th edition rulebook mention those orders destroyed while WD update mention them again, but not destroyed.

reds8n wrote:Going off the FFG stuff, :
No real mention of combat numbers, but it is noted that a deployment of a Palantine and 50 battle sisters is seen as significant on Iocanthos, whilst the largest concentration of the Order Dialogus on Solomon houses a full perceptory of Sisters Dialogus and is guarded by 1000 battle sisters.

Codex: Sisters of Battle, 1997.Pg. 35The Sisterhood is most commonly associated with the Battle Sisters of the Orders Militant, but this is not its only role in the Imperium. There are three other major Orders of the Adepta Sororitas and many others numbering perhaps only a hundred or so individuals each.
[...]
When Sebastian Thor ascended to the position of Ecclesiarchy there were roughly 4,000 Daughters of the Emperor under his command. [...] With recruits passing through the hands of the Schola Progenium once again, the Adepta Sororitas' ranks soon grew to over 10,000 fighers [...]
[...]
Two and a half thousand years later, two more orders were created by Deacis VI (the Orders of the Bloody Rose and Sacred Rose) and the Convent buildings were extended to accommodate almost 15,000 warriors each. In recent years, the number of the Militant Orders' members has declined slightly and each Order now numbers between 3,000 and 4,000 Battle Sisters, of which perhaps 500-750 will be trained as Seraphim. There warriors are spread throughout the galaxy in various battle zones and on extended tours of duty. The size of an Order waxes and wanes irregularly, depending on the quality of recruits available and battle losses. On occasion an Order may number no more than a few hundred warriors, all fighting the enemies of the Emperor, while at other times it may reach a peak of six or seven thousand warriors, with much of the Order fighting in distant wars but still leaving a reserve of several thousand Battle Sisters and Seraphim that can be despatched if needed.

Codex: ArmageddonForce Dispositions in the Third Armageddon War ADEPTA SORORITAS
Order of Our Martyed Lady . . . . . Equiv. 3 Companies
Order of the Argent Shroud . . . . Equiv. 7 Companies

Codex: Witch HuntersPg. 6As numbers within the Orders Militant waxed and waned, varying from a couple of thousand warriors to many thousands, the subsidiary convents began to take on an importance all their own. [...] Though the original six Orders are by far the most numerous and active of the Orders Militant, the new Lesser Orders Militant, or Orders Minoris, became especially useful in the frequent purity sweeps and pogroms instituted by the Witch Hunters.

Codex: Eye of TerrorForce Dispositions at the Outset of the Thirteenth Black Crusade of Abaddon the DespoilerRECORDED ADEPTA SORORITAS
Greater Orders:
Order of the Bloody Rose . . . . . . . . .6 Preceptories
Order of the Ebon Chalice . . . . . . . .4 Preceptories
Order of Our Martyred Lady . . . . . . 5 Preceptories
Lesser Orders
Order of the Ermine Mantle . . . . . . 3 Missions
Order of the Wounded Heart . . . . 1 Commandery
{Nb. Preceptory = "up to 1,000 Battle Sisters", Commandery = "up to 200 Battle Sisters", Mission = "a number of squads". Ref; Codex: Witch Hunters, Pg. 11}

Warhammer: 40,000 main rulebook, 5th edition.Pg. 120There are three major Orders of Adepta Sororitas, the fighting strength of each numbering several thousand warriors, as well as many lesser sisterhoods comprised of around a hundred or so Battle Sisters. An Orders warriors rarely fight as a unit, but instead are commonly spread throughout the galaxy in various battle zones.
{Nb. "Adepta Sororitas" is here used to mean "Battle Sisters of the Orders Militant"}

White Dwarf #380, Chapter Approved: Sisters of BattlePg. 92The Orders Minoris vary in size, and though some only number as few as a hundred or so Battle Sisters[...]