The Dungeon Master's Guide (p. 39) actually addresses this fairly directly:
Modifying XP Awards and Encounter Levels
An orc warband that attacks the PCs by flying over them on primitive hang gliders and dropping large rocks is not the same encounter as one in which
the orcs just charge in with spears. Sometimes, the circumstances give the characters’ opponents a distinct advantage. Other times, the PCs have an advantage. Adjust the XP award and the EL depending on how greatly circumstances change the encounter’s difficulty.
Encounters of EL 2 or lower are the exception. They increase and decrease in proportion to the change in XP. For example, an EL 1 encounter that’s twice as difficult as normal is EL 2, not EL 3.
You can, of course, increase or decrease XP by smaller amounts, such as +10% or –10%, and just eyeball the EL.
Modify all ELs and experience rewards as you see fit, but keep these points in mind.
Experience points drive the game. Don’t be too stingy or too generous.
Most encounters do not need modifying. Don’t waste a lot of time
worrying about the minutiae. Don’t worry about modifying encounters until after you have played the game a while.
Bad rolls or poor choices on the PCs’ part should not modify ELs or XP
awards. If the encounter is difficult because the players were unlucky
or careless, they don’t get more experience.
Just because the PCs are worn down from prior encounters does not mean that later (more difficult) encounters should gain higher awards. Judge the difficulty of an encounter on its own merits.
So, what you do is highly dependent upon whether PC choices or luck led to them having a lower level of equipment. Were you stingy as a DM or did they take actions so as to turn away riches or squander them foolishly? Did they ignore potential treasure or did they have no chance at getting the treasure in the first place?
If it's their fault, they should get nothing extra by a strict interpretation of the rules. If it is your fault, then they are entitled to extra experience for the encounter.
A chart is there for reference, but it is much more clear if you look at it on there rather than here:
\$\begin{array}{|l|c|c|}
\hline
\textbf{Circumstance} & \textbf{XP Award Adjustment} & \textbf{EL Adjustment} \\
\hline
\text{Half as difficult} & \text{XP} \times 1/2 & \text{EL} - 2 \\
\text{Significantly less difficult} & \text{XP} \times 2/3 & \text{EL} - 1 \\
\text{Significantly more difficult} & \text{XP} \times 1\frac{1}{2} & \text{EL} + 1 \\
\text{Twice as difficult} & \text{XP} \times 2 & \text{EL} + 2 \\
\hline
\end{array}
\$
I do think it absolutely needs to be addressed that your players should not be two levels behind in equipment unless they are opting to save up their money for something big rather than be properly equipped for the present.
While there are standard treasures for monster groups, you are absolutely empowered as the DM to add treasure through storyline to bring your players up to par. For example, my players recently raided a bandit camp and were able to take what the bandits stole from their victims as an extra cache. They will also be able to sell bandit scalps to the merchants guild for a bounty. Perhaps a noble rewards them with the wealth filling in the gap for what they perceive to be services rendered to their realm.
This should not be a recurring theme in your campaign unless the players themselves are causing it to happen through their actions, thwarting your attempts to give them the necessary wealth.
Remember that this is an exercise in mutual storytelling - you can bend rules if it increases the enjoyment for all. It doesn't sound like anyone would be happy with such a poor equipment situation - neither you nor the players.