The 2016 Australian Rally Champion had risen to ninth overall on Stage 2, 32:59s off top spot, but only set the 39th-quickest time on the Al Ula to Ha-il special in her South Racing Can-Am.
While the Bikes and Quads were mostly unscathed, the rest of the Dakar field also had to contend with a storm which caused flooding, with the stage cut short due to the inability to operate rescue aircraft.
“Really, a day to forget for us,” said Taylor.
“We got three punctures and we only carry two [spare tyres], so we basically had to sit on the side of the road for over an hour to wait for the spare truck to come with a spare tyre and then we could keep going.
“Then we just had to crawl through – we had no more back-up options – and [it was] super wet, super muddy, visibility was next to zero, so then it was just about survival.
“So, not the best day in the office, but it's a long race and we'll regroup and keep our heads down and fight back tomorrow.”
Taylor's team-mate Cristiano Batista won the stage but Marek Goczal (Energylandia Can-Am) continues to lead overall, by a 9:36s margin to Rodrigo Luppi de Oliveira in another of the South Racing Can-Ams.
Martin Macik (MM Technology) hit back in the Trucks with a win on Stage 3 but the time he lost on the day prior means that the Czech is still over 54 minutes off top spot overall.
Tatra Buggyra ZM Racing's Jaroslav Valtr now holds sway by 5:45s after previous event leader, Ales Loprais (Instaforex Loprais Praga) was issued a 15-minute penalty.
In Quads, Alexandre Giroud (Yamaha Racing – SMX – Drag'on) has skipped 35:31s clear of the field with another stage win, while Lightweight Prototype is now headed by Seth Quintero (Red Bull Off-Road JR Team USA by BFG) after Francisco Lopez Contardo (Red Bull Can-Am) lost more than an hour.
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CLICK HERE for Cars report
CLICK HERE for extended highlights of Stage 3