Short answer. In most cases yes, because the fees are not forgiven but deferred. The docket and other lawful fees you were excused from paying become a lien on any judgment rendered in your favour, so they come out of what you recover unless the court provides otherwise.
What the law says
The amount of the docket and other lawful fees which the indigent was exempted from paying shall be a lien on any judgment rendered in the case favorable to the indigent, unless the court otherwise provides.
Rule 3, Section 21 — Indigent party. Read the full provision →
What the exemption actually covers
Being authorised to litigate as an indigent is an exemption from what the court itself charges, not a discount on anything else. The authority covers docket and other lawful fees, and also the cost of transcripts of stenographic notes that the court may order to be furnished to you. That second item is worth more than people expect, because transcripts in a long trial can cost more than the filing fee did. What the authority does not do is erase the amounts. The rule treats them as suspended while the case runs, then settles up at the end out of whatever the judgment gives you.
Why it is called a lien, and what that means for your award
A lien is a charge that attaches to the money before it reaches you. If you are awarded a sum after winning, the exempted fees are deducted from that award rather than billed to you separately. If you lose, there is no judgment in your favour for the lien to attach to. The rule adds the words unless the court otherwise provides, which leaves the judge room to relieve a winning party of the charge where circumstances warrant it. That relief is discretionary, not automatic, so it is not something to count on when deciding whether to sue.
A separate and harsher risk
The rule has a second path that does not wait for judgment at all. If the court determines after hearing that the party declared as an indigent is in fact a person with sufficient income or property, the proper docket and other lawful fees are assessed and collected by the clerk of court. This does not depend on winning or losing. If payment is not made within the time the court fixes, execution issues for it, and the rule expressly preserves such other sanctions as the court may impose. Understating your means to obtain the exemption is therefore an expensive gamble.
How to plan around it
Treat the exemption as a cash-flow measure rather than as free litigation. When you weigh whether a claim is worth bringing, count the deferred fees against the amount you realistically expect to recover, because they come off the top of it. Keep the proof of your circumstances, meaning the income and property position you put before the court on the ex parte application, because an adverse party may contest the grant at any time before judgment is rendered by the trial court and you may have to make that showing more than once.