I most frequently use the ISR/TS2009 (The Institute for Scriptural Research's "The Scriptures" 2009 version) when doing bible study because of it's high accuracy in translating what can be translated and refusal to translate what shouldn't (personal names, place names, names of God, etc). Here's what it says:
28) And Elohim blessed them, and Elohim said to them, “Bear fruit and increase, and fill the earth and subdue it, and rule over the fish of the sea, and over the birds of the heavens, and over all creatures moving on the earth.”
This is the first of the mitzvot God gives man, making it one of the most important to understand. So, let's take it piece by piece:
Strong's # Hebrew Transliteration Common translation Grammatical morphology
6509 פְּר֥וּ pə-rū Be fruitful Exhortative verb, imperative, masculine plural
7235 וּרְב֛וּ ū-rə-ḇū and multiply Conjunctive-waw + Exhortative verb, imperative, masculine plural
4390 וּמִלְא֥וּ ū-mil-’ū and fill Conjunctive-waw + Exhortative verb, imperative, masculine plural
853 אֶת־ ’eṯ- Direct object marker
776 הָאָ֖רֶץ hā-’ā-reṣ the earth Article + Noun, feminine singular
Okay, that's a lot of linguistics, but don't worry, I'll walk you through it. An exhortative, imperative verb is when you are telling someone to do a thing, but not commanding them to do so. For example, when you shout, "Look out!" you aren't commanding the person to do a thing (or else), but advising them of their best interests. This is how we can understand the line to be a mitzvah. That is, God isn't saying, "Be fruitful or else," but, "Be fruitful, for your sake." The root of this word is, "to bear fruit." So, the best we can translate the idea into English is, "Bear fruit," with the understanding that the imperative form is for our sake.
The "ū" before our next word links the verbs together. For example, in the sentence, "I love to eat pumpkin pie," the verbs "love" and "eat" are linked together. In English we don't have a way to say "bear fruit-increase" so this is translated as "bear fruit and increase." The core of this word is rabah, which literally means "bring in abundance" and thus is best translated to "increase." "Multiply" limits the meaning to "manifold increase" when it is equally likely this could have meant "increase incrementally" ("addition") or "increase hyperbolically" ("exponentially"). Because the verbs are linked, the exhortative imperative remains.
The next verb is the crux of your question, and it is also linked to the previous verbs by "ū" and remains an exhortative imperative. The root, male (pronounced "maw-lay") means "to fill," or at times can be translated as "to be full." It also has the connotations of "to accomplish (by having filled)" and "satisfy," that is, "filled to a sufficiency." This differs from "fill entirely." For example, a "full" (male) glass isn't filled to the brim and being full (male) from a meal would mean that one's hunger is sated, not the way we imagine being full after Thanksgiving dinner or a buffet. My knowledge of Hebrew is not exhaustive, but I cannot find any scriptural usage of a Hebrew verb for the concept of "to refill" or "to fill again."
אֶת־ & הָאָ֖רֶץ
So far we've only had verbs. Since the sentence is an imperative, we know the subject is "you" or "the person to whom I am speaking." We can also understand the object of "bear" to be "fruit" because the concepts are yoked together. From context we can understand the object of "increase" to be "the amount of people." But, "fill" requires the mention of the container being filled. So, ’eṯ tells us, "the next word is the object of the previous verb." And finally, that object itself is hā-’ā-reṣ: formed from ha, "the," and erets, "land/earth."
So, the best we can translate this mitzvah is "Bear fruit, increase, and fill the land." From our deeper understanding of the Hebrew language we see that the mitzvah doesn't imply that the Earth was previously filled nor that God wants us to "overfill" the Earth. It also shows us that this is something that will benefit those to whom God is speaking (though, who that is limited to is up for debate), but is not something for which God would punish one for "disobeying." This is one of many ways the receiver of the mitzvah can help or punish themself.
Conclusion, no, this verse does not imply that the earth was previously filled and this misinterpretation could have been avoided by comparing translations. Perhaps now knowing this will aid your further studies.